❌ sarek/test_full_germline_aws failed 😿 Run Name sarek_test_full_germline_aws Duration 4h 14m 21s Status ❌ Failed Error Message

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/tmp/Bazel.runfiles_c13kj3j0/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)
I1015 22:21:34.260703 139736641774016 make_examples_core.py:3855] model.example_info filename: /opt/models/wgs/model.example_info.json
I1015 22:21:34.261097 139736641774016 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wgs/model.example_info.json
I1015 22:21:34.261528 139736641774016 make_examples_core.py:3876] Flags for calling:
call_small_model_examples: True
pileup_image_height: 100
pileup_image_width: 221
small_model_indel_gq_threshold: 28
small_model_snp_gq_threshold: 20
small_model_vaf_context_window_size: 51
track_ref_reads: True
trained_small_model_path: /opt/smallmodels/wgs/model.keras
W1015 22:21:34.261647 139736641774016 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]
I1015 22:21:34.265194 139736641774016 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].
I1015 22:21:34.265471 139736641774016 make_examples_options.py:1233] Parsing AUX Fields: []
W1015 22:21:34.265892 139736641774016 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1015 22:21:34.272867 139736641774016 make_examples_core.py:384] Task 0/12: Preparing inputs
I1015 22:21:34.329897 139736641774016 genomics_reader.py:223] Reading NA12878.recal.cram with NativeSamReader
I1015 22:21:34.361066 140277624431040 make_examples_core.py:384] Task 2/12: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', '...

Command Line

nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws -params-file '<https://api.cloud.seqera.io/ephemeral/yNYcZFD4tgrgUznOb4aB1w.json>' -with-tower -r dev -profile test_full_germline_aws

Oct 15, 2026 at 10:22 PM