:x: sarek/test_full_germline_aws failed :crying_ca...
# sarek_devf
Full test notifications
06/11/2026, 9:41 PM❌ sarek/test_full_germline_aws failed 😿 Run Name
sarek_test_full_germline_aws Duration
4h 52m 14s Status
❌ Failed Error Message
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9:40PM INF [seqera-fusion] setting up AWS Batch spot instance monitoring provider=aws-batch
9:40PM INF [seqera-fusion] instance metadata ami-id=ami-0acc5dd6b31082def instance-id=i-0e44854321dbc9754 instance-type=c6id.32xlarge
9:40PM INF [seqera-fusion] starting incremental snapshot timer interval=300000
grep: write error: Broken pipe
2026-06-11 21:40:07.718779: I tensorflow/core/util/port.cc:110] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable `TF_ENABLE_ONEDNN_OPTS=0`.
2026-06-11 21:40:07.720494: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2026-06-11 21:40:07.756210: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
2026-06-11 21:40:07.756593: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
To enable the following instructions: AVX2 AVX512F AVX512_VNNI FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
2026-06-11 21:40:08.609777: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
I0611 21:40:09.715597 140180420981184 run_deepvariant.py:635] Creating a directory for intermediate results in tmp
***** Intermediate results will be written to tmp in docker. ****
***** Running the command:*****
time seq 0 11 | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "Homo_sapiens_assembly38.fasta" --reads "NA12878.recal.cram" --examples "tmp/make_examples.tfrecord@12.gz" --checkpoint "/opt/models/wgs" --call_small_model_examples --gvcf "tmp/gvcf.tfrecord@12.gz" --regions "chr15_20729747-21193490.bed" --sample_name "NA12878" --small_model_indel_gq_threshold "28" --small_model_snp_gq_... Copy code
nextflow run '<https://github.com/nf-core/sarek>' -name sarek_test_full_germline_aws -params-file '<https://api.cloud.seqera.io/ephemeral/CPltA2fT6cuZZ6dmPFwOkw.json>' -with-tower -r 375c449933215d19e26f645fd61c5bc38580e2da -profile test_full_germline_aws😿 1