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nf-core

:x: *sarek/test_full_germline_ncbench_agilent* failed :crying_cat_face: *Run Name*
sarek_test_full_germline_ncbench_agilent *Duration*
2h 24m 17s *Status*
:x: Failed *Error Message*
```(more omitted..)
/tmp/Bazel.runfiles_c831esgf/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 15:08:23.998646 140510336061888 make_examples_core.py:3855] model.example_info filename: /opt/models/wes/model.example_info.json
I1109 15:08:23.998920 140510336061888 make_examples_core.py:3859] Reading flags_for_calling from /opt/models/wes/model.example_info.json
I1109 15:08:23.999157 140510336061888 make_examples_core.py:3876] Flags for calling:
pileup_image_height: 100
pileup_image_width: 221
I1109 15:08:24.006853 140135731941824 genomics_reader.py:223] Reading NA12878_200M.recal.cram with NativeSamReader
I1109 15:08:24.001604 140510336061888 dv_utils.py:333] From /opt/models/wes/model.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1109 15:08:24.001847 140510336061888 make_examples_options.py:1233] Parsing AUX Fields: []
W1109 15:08:24.002128 140510336061888 make_examples_options.py:1284] Automatically setting --trim_reads_for_pileup to True because --alt_aligned_pileup is set.
I1109 15:08:24.004658 140510336061888 make_examples_core.py:384] Task 4/12: Preparing inputs
I1109 15:08:24.026751 140510336061888 genomics_reader.py:223] Reading NA12878_200M.recal.cram with NativeSamReader
I1109 15:08:24.312843 139717381923264 make_examples_core.py:384] Task 1/12: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM']
I1109 15:08:24.370161 139628260233664 make_examples_core.py:384] Task 8/12: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr...``` *Command Line*
```nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_ncbench_agilent -params-file '<https://api.cloud.seqera.io/ephemeral/gHOi4TlyofZjTERLYmlOjA.json>' -with-tower -r dev -profile test_full_germline_ncbench_agilent``` Nov 9, 2026 at 3:09 PM