Arvados

We got the following error while attempting to submit a workflow using arvados-cwl-runner (a-c-r):

$ arvados-cwl-runner --eval-timeout 10 --submit-runner-ram 8192 --submit --no-wait --api=containers ../workflows/gatk-4.0.0.0-joint-calling.cwl interval-147-2017may17-eglyx.joint_calling_inputs.diploid.yaml
2018-05-23 12:07:37 cwltool INFO: /usr/bin/arvados-cwl-runner 1.1.4.20180510154117, arvados-python-client 1.1.4.20180510153813, cwltool 1.0.20180508202931
2018-05-23 12:07:37 cwltool INFO: Resolved '../workflows/gatk-4.0.0.0-joint-calling.cwl' to 'file:///home/mercury/checkouts/arvados-datasets/15x/workflows/gatk-4.0.0.0-joint-calling.cwl'
2018-05-23 12:09:14 cwltool WARNING: Workflow checker warning:
../workflows/gatk-4.0.0.0-genomics-db-and-genotypegvcfs-per-interval.cwl:75:9: Source
                                                                               'variant-index' of
                                                                               type ["null",
                                                                               "File"] may be
                                                                               incompatible
../workflows/gatk-4.0.0.0-genomics-db-and-genotypegvcfs-per-interval.cwl:80:7:   with sink
                                                                                 'secondary_files'
                                                                                 of type ["File",
                                                                                 {"type": "array",
                                                                                 "items": "File"}]
../workflows/gatk-4.0.0.0-genomics-db-and-genotypegvcfs-per-interval.cwl:61:7: Sink 'reference'
../tools/gatk-4.0/GenotypeGVCFs.cwl:149:3:                                       expects
                                                                                 secondaryFiles:
                                                                                 ['.fai', '^.dict']
                                                                                 but
../workflows/gatk-4.0.0.0-genomics-db-and-genotypegvcfs-per-interval.cwl:26:3:   source
                                                                                 'reference' does
                                                                                 not include
                                                                                 secondaryFiles.
                                                                                 To fix, add
                                                                                 secondaryFiles:
                                                                                 ['.fai', '^.dict']
                                                                                 to definition of
                                                                                 'reference'.
2018-05-23 12:50:12 cwltool ERROR: Unhandled error, try again with --debug for more information:
  <HttpError 422 when requesting https://arvados-api-eglyx.hgi.sanger.ac.uk/arvados/v1/collections?ensure_unique_name=true&alt=json returned "#<PG::InFailedSqlTransaction: ERROR:  current transaction is aborted, commands ignored until end of transaction block
>">