❌ sarek/test_full_germline_aws failed 😿 Run Name sarek_test_full_germline_aws Duration 4h 23m 40s Status ❌ Failed Error Message

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track_ref_reads: True
trained_small_model_path: /opt/smallmodels/wgs/model.keras
W1109 17:07:42.969958 140346294792640 make_examples_core.py:3890] Flag call_small_model_examples is specified in model.example_info.json [True] but overridden by command line with value [True]
I1109 17:07:42.974511 140346294792640 dv_utils.py:333] From /opt/models/wgs/model.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1109 17:07:42.974930 140346294792640 make_examples_options.py:1233] Parsing AUX Fields: []
W1109 17:07:42.975501 140346294792640 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1109 17:07:42.975967 140260061249984 make_examples_core.py:384] Task 10/12: Preparing inputs
I1109 17:07:42.981956 140346294792640 make_examples_core.py:384] Task 5/12: Preparing inputs
I1109 17:07:43.035340 140639212265920 genomics_reader.py:223] Reading chr15_20729747-21193490.bed with NativeBedReader
I1109 17:07:43.069675 140346294792640 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I1109 17:07:43.068404 140341084332480 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I1109 17:07:43.082329 140260061249984 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
/tmp/Bazel.runfiles_eh9efyke/runfiles/absl_py/absl/flags/_validators.py:233: UserWarning: Flag --mode has a non-None default value; therefore, mark_flag_as_required will pass even if flag is not specified in the command line!
  mark_flag_as_required(flag_name, flag_values)
I1109 17:07:43.139967 140282452140480 genomics_reader.py:223] Reading chr15_20729747-21193490.bed with NativeBedReader
I1109 17:07:43.139361 140664471617984 make_examples_core.py:3855] model.example_info filename: /opt/models/wgs/model.example_info.json
I1109 17:07:43.139914 140664471617984 make_examples_core.py:3859] Reading flags_for_calling from /op...

Command Line

nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws -params-file '<https://api.cloud.seqera.io/ephemeral/oHO2SJGD3XLlmfSxtXg9xA.json>' -with-tower -r dev -profile test_full_germline_aws

Nov 9, 2026 at 5:08 PM