:x: sarek/test_full_aws failed :crying_cat_face: R...
# sarek_devf
Full test notifications
10/27/2026, 10:28 AM❌ sarek/test_full_aws failed 😿 Run Name
adoring_stone Duration
1h 58m 21s Status
❌ Failed Error Message
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W1027 10:28:03.534462 140546465968576 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1027 10:28:03.535759 140546465968576 make_examples_core.py:384] Task 9/12: Preparing inputs
I1027 10:28:03.566453 140546465968576 genomics_reader.py:223] Reading HCC1395T.recal.cram with NativeSamReader
/tmp/Bazel.runfiles_s287u9lq/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)
I1027 10:28:03.471638 140513094275520 make_examples_core.py:3855] model.example_info filename: /opt/models/deepsomatic/wes/model.example_info.json
I1027 10:28:03.472012 140513094275520 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/deepsomatic/wes/model.example_info.json
I1027 10:28:03.472353 140513094275520 make_examples_core.py:3876] Flags for calling:
vsc_min_fraction_indels: 0.05
vsc_min_fraction_snps: 0.029
vsc_max_fraction_indels_for_non_target_sample: 0.5
vsc_max_fraction_snps_for_non_target_sample: 0.5
I1027 10:28:03.492679 140513094275520 genomics_reader.py:223] Reading HCC1395N.recal.cram with NativeSamReader
I1027 10:28:03.516201 140513094275520 genomics_reader.py:223] Reading HCC1395T.recal.cram with NativeSamReader
I1027 10:28:03.520451 140513094275520 dv_utils.py:333] From /opt/models/deepsomatic/wes/model.example_info.json: Shape of input examples: [200, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1027 10:28:03.520816 140513094275520 make_examples_options.py:1233] Parsing AUX Fields: []
W1027 10:28:03.521284 140513094275520 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1027 10:28:03.523530 140513094275520 make_examples_core.py:384] Task 4/12: Preparing inputs
I1027 10:28:03.559457 14051309427... Copy code
nextflow run '<https://github.com/nf-core/sarek>' -name adoring_stone -params-file '<https://api.cloud.seqera.io/ephemeral/DLUS8eDXTse0XqWW4i4iyQ.json>' -with-tower -r 6e9b164daa2a54c98f7dda538645d340c561ac24 -profile test_full_aws🫠 1