Dear BraTS team,
My submission (ID: 9713950) has encountered an error during scoring. This is the log file. Please clarify this for me.
TDERR: 2021-08-11T01:24:48.813324181Z d1a471e60f04 2021-08-11 01:24:48,813 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/validation-phase-workflow.cwl'
STDERR: 2021-08-11T01:24:54.101030014Z d1a471e60f04 2021-08-11 01:24:54,100 MainThread WARNING cwltool: Workflow checker warning:
STDERR: 2021-08-11T01:24:54.101061004Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-11T01:24:54.101065154Z ["null", "File"] may be
STDERR: 2021-08-11T01:24:54.101069040Z incompatible
STDERR: 2021-08-11T01:24:54.101072523Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:75:9: with sink 'input_file' of
STDERR: 2021-08-11T01:24:54.101076132Z type "File"
STDERR: 2021-08-11T01:24:54.101080026Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:55:9: Source 'filepath' of type
STDERR: 2021-08-11T01:24:54.101083464Z ["null", "File"] may be
STDERR: 2021-08-11T01:24:54.101086886Z incompatible
STDERR: 2021-08-11T01:24:54.101090168Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:135:9: with sink 'input_file' of
STDERR: 2021-08-11T01:24:54.101093434Z type "File"
STDERR: 2021-08-11T01:24:55.508597781Z d1a471e60f04 2021-08-11 01:24:55,508 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2021-08-11T01:24:56.638073047Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpzjols7ct/worker_log.txt
STDERR: 2021-08-11T01:24:57.211607896Z d1a471e60f04 2021-08-11 01:24:57,211 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run
STDERR: 2021-08-11T01:24:57.212965765Z d1a471e60f04 2021-08-11 01:24:57,212 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_get_submission.cwl/instance-v9itkzh_ with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:24:57.213229797Z d1a471e60f04 2021-08-11 01:24:57,213 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-c_xpgxe2 with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:24:57.213415264Z d1a471e60f04 2021-08-11 01:24:57,213 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_set_permissions.cwl/instance-uo_5ou57 with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:24:58.431447061Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmp1v96v6ba/worker_log.txt
STDERR: 2021-08-11T01:24:58.511597697Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpp42t9z85/worker_log.txt
STDERR: 2021-08-11T01:24:58.586220792Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmp6ktagiw7/worker_log.txt
STDERR: 2021-08-11T01:27:47.454445953Z d1a471e60f04 2021-08-11 01:27:47,451 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/cwl-tool-synapseclient/v1.4/cwl/synapse-get-tool.cwl#synapse-get' synapse kind-https_raw.githubusercontent.com_Sage-Bionetworks-Workflows_cwl-tool-synapseclient_v1.4_cwl_synapse-get-tool.cwl_synapse-get/instance-c_xpgxe2
STDERR: 2021-08-11T01:28:18.882146149Z d1a471e60f04 2021-08-11 01:28:18,881 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/get_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_get_submission.cwl/instance-v9itkzh_
STDERR: 2021-08-11T01:28:18.882842506Z d1a471e60f04 2021-08-11 01:28:18,882 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_validate.cwl/instance-h8n1cc2n with job batch system ID: 4 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:28:19.636418737Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpf5lws1xv/worker_log.txt
STDERR: 2021-08-11T01:28:23.565751314Z d1a471e60f04 2021-08-11 01:28:23,565 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/set_permissions.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_set_permissions.cwl/instance-uo_5ou57
STDERR: 2021-08-11T01:29:58.456784491Z d1a471e60f04 2021-08-11 01:29:58,456 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_validate.cwl/instance-h8n1cc2n
STDERR: 2021-08-11T01:29:58.457489404Z d1a471e60f04 2021-08-11 01:29:58,457 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_validate_email.cwl/instance-am8f_e1p with job batch system ID: 5 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:29:58.457594170Z d1a471e60f04 2021-08-11 01:29:58,457 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-cor7ebtk with job batch system ID: 6 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:29:59.375900637Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpm_ov2hez/worker_log.txt
STDERR: 2021-08-11T01:29:59.500532094Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpbj2tsp0v/worker_log.txt
STDERR: 2021-08-11T01:31:51.781693547Z d1a471e60f04 2021-08-11 01:31:51,781 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-cor7ebtk
STDERR: 2021-08-11T01:31:57.476139244Z d1a471e60f04 2021-08-11 01:31:57,475 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_validate_email.cwl/instance-am8f_e1p
STDERR: 2021-08-11T01:31:57.476685417Z d1a471e60f04 2021-08-11 01:31:57,476 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-szknyxy2 with job batch system ID: 7 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:31:58.324890065Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmp130f1epx/worker_log.txt
STDERR: 2021-08-11T01:31:58.740784818Z d1a471e60f04 2021-08-11 01:31:58,740 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-szknyxy2
STDERR: 2021-08-11T01:31:58.741679279Z d1a471e60f04 2021-08-11 01:31:58,741 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_score.cwl/instance-qqkdl3fa with job batch system ID: 8 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:31:59.513717490Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmp_t3910q5/worker_log.txt
STDERR: 2021-08-11T01:33:55.087920671Z d1a471e60f04 2021-08-11 01:33:55,087 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_score.cwl/instance-qqkdl3fa
STDERR: 2021-08-11T01:33:55.088701265Z d1a471e60f04 2021-08-11 01:33:55,088 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-2kdhxg2k with job batch system ID: 9 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:33:55.088879139Z d1a471e60f04 2021-08-11 01:33:55,088 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_score_email.cwl/instance-uwyqfcqe with job batch system ID: 10 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:33:56.125795857Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmp815qpjym/worker_log.txt
STDERR: 2021-08-11T01:33:56.260969194Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpgd2vdh0e/worker_log.txt
STDERR: 2021-08-11T01:35:31.294754889Z d1a471e60f04 2021-08-11 01:35:31,294 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-2kdhxg2k
STDERR: 2021-08-11T01:35:35.842537615Z d1a471e60f04 2021-08-11 01:35:35,842 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/score_email.cwl' python3 kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_score_email.cwl/instance-uwyqfcqe
STDERR: 2021-08-11T01:35:35.843085161Z d1a471e60f04 2021-08-11 01:35:35,842 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_score.cwl/instance-qqkdl3fa with job batch system ID: 11 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:35:36.826468099Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpxipm93bu/worker_log.txt
STDERR: 2021-08-11T01:35:37.048822768Z d1a471e60f04 2021-08-11 01:35:37,048 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/brats-dream-challenge-infra-main/score.cwl' score.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_06cb663a-e117-457f-9721-47d15b6e5c8d_brats-dream-challenge-infra-main_score.cwl/instance-qqkdl3fa
STDERR: 2021-08-11T01:35:37.049686682Z d1a471e60f04 2021-08-11 01:35:37,049 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-szknyxy2 with job batch system ID: 12 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:35:38.006199813Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpoq4uotpa/worker_log.txt
STDERR: 2021-08-11T01:35:38.242388740Z d1a471e60f04 2021-08-11 01:35:38,241 MainThread INFO toil.leader: Job ended: 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/check_status.cwl' kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_check_status.cwl/instance-szknyxy2
STDERR: 2021-08-11T01:35:38.243003725Z d1a471e60f04 2021-08-11 01:35:38,242 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/annotate_submission.cwl' challengeutils kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_annotate_submission.cwl/instance-cor7ebtk with job batch system ID: 13 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:35:38.243177757Z d1a471e60f04 2021-08-11 01:35:38,243 MainThread INFO toil.leader: Issued job 'https://raw.githubusercontent.com/Sage-Bionetworks/ChallengeWorkflowTemplates/v3.1/cwl/validate_email.cwl' python3 kind-https_raw.githubusercontent.com_Sage-Bionetworks_ChallengeWorkflowTemplates_v3.1_cwl_validate_email.cwl/instance-am8f_e1p with job batch system ID: 14 and cores: 1, disk: 1.0 G, and memory: 100.0 M
STDERR: 2021-08-11T01:35:39.228251944Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/06cb663a-e117-457f-9721-47d15b6e5c8d/node-b21951e1-fbba-4fee-b4f0-b9e95d5b30d1-16349ee66b573b0d6cff3dbc6912349f/tmpy0q7r2lw/worker_log.txt
STDERR: 2021-08-11T01:35:39.315
Created by khue @khue thanks for your reply. I have also submitted. I Will let you know if I find the solution. Thanks for your reply. @Virendra , I found an error in my code that causes the shape of my submission to (240,155, 240), which is wrong. The correct should be (240, 240, 155). I reshape the files and resubmit them, now it's in the queue so I don't know if the problem is solved yet. @khue Are you able to sort out your problem? if yes, then please let us know. Thanks.
@vchung : How to solve origin mismatch? I didn't get you. Thanks for your reply. @vchung , thank you very much! Dear @khue ,
Your submission, 9713950, cannot be properly scored due to the images not being aligned with the reference, specifically, there is a size mismatch.
@Virendra ,
Your submission, 9713949, can also not be scored, as there is an origin mismatch between your images and the references. I am facing the same issue. My submission ID is 9713949. Please help. I have followed all the instructions, as advised on the web.
Drop files to upload
Submission Status ACCEPTED - Prediction File Status INVALID page is loading…