Dear BraTS team, I have placed all segmented outputs (.nii.gz format) in a directory and then compressing the directory as .tar.gz , then uploaded here. The encountered error in the log file is," STDERR: 2021-08-02T22:58:14.466533889Z 7f7c3083c323 2021-08-02 22:58:14,466 MainThread INFO cwltool: Resolved '/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' to 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validation-phase-workflow.cwl' STDERR: 2021-08-02T22:58:17.476146097Z 7f7c3083c323 2021-08-02 22:58:17,475 MainThread WARNING cwltool: Workflow checker warning: STDERR: 2021-08-02T22:58:17.476185981Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-02T22:58:17.476190551Z ["null", "File"] may be STDERR: 2021-08-02T22:58:17.476194472Z incompatible STDERR: 2021-08-02T22:58:17.476198019Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:62:9: with sink 'input_file' of STDERR: 2021-08-02T22:58:17.476201359Z type "File" STDERR: 2021-08-02T22:58:17.476205025Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:42:9: Source 'filepath' of type STDERR: 2021-08-02T22:58:17.476208184Z ["null", "File"] may be STDERR: 2021-08-02T22:58:17.476211581Z incompatible STDERR: 2021-08-02T22:58:17.476214576Z brats-dream-challenge-infra-main/validation-phase-workflow.cwl:122:9: with sink 'input_file' of STDERR: 2021-08-02T22:58:17.476217731Z type "File" STDERR: 2021-08-02T22:58:19.302888567Z 7f7c3083c323 2021-08-02 22:58:19,302 MainThread INFO toil: Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-02T22:58:20.408515806Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmpxvzzxqsa/worker_log.txt STDERR: 2021-08-02T22:58:20.689779757Z 7f7c3083c323 2021-08-02 22:58:20,689 MainThread INFO toil.leader: 0 jobs are running, 0 jobs are issued and waiting to run STDERR: 2021-08-02T22:58:20.690559771Z 7f7c3083c323 2021-08-02 22:58:20,690 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-d5prkwgk with job batch system ID: 1 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T22:58:20.690773799Z 7f7c3083c323 2021-08-02 22:58:20,690 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-6o3cnmtr with job batch system ID: 2 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T22:58:21.780591841Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmprhvk4k2g/worker_log.txt STDERR: 2021-08-02T22:58:21.844677797Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmpr6jw4jfl/worker_log.txt STDERR: 2021-08-02T22:58:25.318461772Z 7f7c3083c323 2021-08-02 22:58:25,316 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-6o3cnmtr STDERR: 2021-08-02T22:58:25.459237943Z 7f7c3083c323 2021-08-02 22:58:25,459 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-d5prkwgk STDERR: 2021-08-02T22:58:25.459923365Z 7f7c3083c323 2021-08-02 22:58:25,459 MainThread INFO toil.leader: Issued job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m with job batch system ID: 3 and cores: 1, disk: 1.0 G, and memory: 100.0 M STDERR: 2021-08-02T22:58:26.182659403Z INFO:toil.worker:Redirecting logging to /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/worker_log.txt STDERR: 2021-08-02T22:58:27.571837995Z 7f7c3083c323 2021-08-02 22:58:27,571 MainThread INFO toil.leader: Job ended: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m STDERR: 2021-08-02T22:58:27.572344196Z 7f7c3083c323 2021-08-02 22:58:27,572 MainThread WARNING toil.leader: The job seems to have left a log file, indicating failure: 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m STDERR: 2021-08-02T22:58:27.572625962Z 7f7c3083c323 2021-08-02 22:58:27,572 MainThread WARNING toil.leader: Log from job kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m follows: STDERR: 2021-08-02T22:58:27.572636230Z =========> STDERR: 2021-08-02T22:58:27.572640130Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-02T22:58:27.572643467Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-02T22:58:27.572647241Z [job validate.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-02T22:58:27.572662943Z WARNING:cwltool:[job validate.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-02T22:58:27.572666921Z [job validate.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk$ docker \ STDERR: 2021-08-02T22:58:27.572670956Z run \ STDERR: 2021-08-02T22:58:27.572673937Z -i \ STDERR: 2021-08-02T22:58:27.572677139Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk,target=/ZVUwcp \ STDERR: 2021-08-02T22:58:27.572681107Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_bw68fn6wm,target=/tmp \ STDERR: 2021-08-02T22:58:27.572685523Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmpigk4fjps.tmp,target=/var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991,readonly \ STDERR: 2021-08-02T22:58:27.572689958Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmplg34vtex.tmp,target=/var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T22:58:27.572694352Z --workdir=/ZVUwcp \ STDERR: 2021-08-02T22:58:27.572697626Z --read-only=true \ STDERR: 2021-08-02T22:58:27.572701037Z --user=0:0 \ STDERR: 2021-08-02T22:58:27.572704359Z --rm \ STDERR: 2021-08-02T22:58:27.572707614Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T22:58:27.572710803Z --env=HOME=/ZVUwcp \ STDERR: 2021-08-02T22:58:27.572714110Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_b_g3mmhte/20210802225826-255483.cid \ STDERR: 2021-08-02T22:58:27.572718367Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T22:58:27.572721891Z validate.py \ STDERR: 2021-08-02T22:58:27.572724949Z -p \ STDERR: 2021-08-02T22:58:27.572728147Z /var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991 \ STDERR: 2021-08-02T22:58:27.572731394Z -g \ STDERR: 2021-08-02T22:58:27.572734473Z /var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T22:58:27.572741101Z -e \ STDERR: 2021-08-02T22:58:27.572744259Z org.sagebionetworks.repo.model.FileEntity \ STDERR: 2021-08-02T22:58:27.572747203Z -o \ STDERR: 2021-08-02T22:58:27.572750287Z results.json STDERR: 2021-08-02T22:58:27.572753388Z INFO:cwltool:[job validate.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk$ docker \ STDERR: 2021-08-02T22:58:27.572757670Z run \ STDERR: 2021-08-02T22:58:27.572761015Z -i \ STDERR: 2021-08-02T22:58:27.572764036Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk,target=/ZVUwcp \ STDERR: 2021-08-02T22:58:27.572821781Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_bw68fn6wm,target=/tmp \ STDERR: 2021-08-02T22:58:27.572828695Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmpigk4fjps.tmp,target=/var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991,readonly \ STDERR: 2021-08-02T22:58:27.572832843Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmplg34vtex.tmp,target=/var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T22:58:27.572836939Z --workdir=/ZVUwcp \ STDERR: 2021-08-02T22:58:27.572839241Z --read-only=true \ STDERR: 2021-08-02T22:58:27.572841732Z --user=0:0 \ STDERR: 2021-08-02T22:58:27.572843847Z --rm \ STDERR: 2021-08-02T22:58:27.572846771Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T22:58:27.572849816Z --env=HOME=/ZVUwcp \ STDERR: 2021-08-02T22:58:27.572853266Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_b_g3mmhte/20210802225826-255483.cid \ STDERR: 2021-08-02T22:58:27.572857233Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T22:58:27.572860447Z validate.py \ STDERR: 2021-08-02T22:58:27.572863568Z -p \ STDERR: 2021-08-02T22:58:27.572866716Z /var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991 \ STDERR: 2021-08-02T22:58:27.572870307Z -g \ STDERR: 2021-08-02T22:58:27.572878604Z /var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T22:58:27.572881203Z -e \ STDERR: 2021-08-02T22:58:27.572883408Z org.sagebionetworks.repo.model.FileEntity \ STDERR: 2021-08-02T22:58:27.572885553Z -o \ STDERR: 2021-08-02T22:58:27.572887585Z results.json STDERR: 2021-08-02T22:58:27.572889712Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:27.572891956Z File "/usr/local/lib/python3.6/tarfile.py", line 188, in nti STDERR: 2021-08-02T22:58:27.572894308Z s = nts(s, "ascii", "strict") STDERR: 2021-08-02T22:58:27.572896659Z File "/usr/local/lib/python3.6/tarfile.py", line 172, in nts STDERR: 2021-08-02T22:58:27.572899147Z return s.decode(encoding, errors) STDERR: 2021-08-02T22:58:27.572901477Z UnicodeDecodeError: 'ascii' codec can't decode byte 0xbc in position 1: ordinal not in range(128) STDERR: 2021-08-02T22:58:27.572903827Z STDERR: 2021-08-02T22:58:27.572906000Z During handling of the above exception, another exception occurred: STDERR: 2021-08-02T22:58:27.572908236Z STDERR: 2021-08-02T22:58:27.572910266Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:27.572912852Z File "/usr/local/lib/python3.6/tarfile.py", line 2294, in next STDERR: 2021-08-02T22:58:27.572915102Z tarinfo = self.tarinfo.fromtarfile(self) STDERR: 2021-08-02T22:58:27.572917284Z File "/usr/local/lib/python3.6/tarfile.py", line 1090, in fromtarfile STDERR: 2021-08-02T22:58:27.572919597Z obj = cls.frombuf(buf, tarfile.encoding, tarfile.errors) STDERR: 2021-08-02T22:58:27.572921780Z File "/usr/local/lib/python3.6/tarfile.py", line 1032, in frombuf STDERR: 2021-08-02T22:58:27.572924050Z chksum = nti(buf[148:156]) STDERR: 2021-08-02T22:58:27.572926177Z File "/usr/local/lib/python3.6/tarfile.py", line 191, in nti STDERR: 2021-08-02T22:58:27.572928491Z raise InvalidHeaderError("invalid header") STDERR: 2021-08-02T22:58:27.572930693Z tarfile.InvalidHeaderError: invalid header STDERR: 2021-08-02T22:58:27.572933373Z STDERR: 2021-08-02T22:58:27.572936371Z During handling of the above exception, another exception occurred: STDERR: 2021-08-02T22:58:27.572939596Z STDERR: 2021-08-02T22:58:27.572942533Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:27.572945598Z File "/usr/local/bin/validate.py", line 130, in STDERR: 2021-08-02T22:58:27.572949132Z main() STDERR: 2021-08-02T22:58:27.572952260Z File "/usr/local/bin/validate.py", line 108, in main STDERR: 2021-08-02T22:58:27.572955216Z preds = get_images(args.predictions_file) STDERR: 2021-08-02T22:58:27.572957372Z File "/usr/local/bin/validate.py", line 36, in get_images STDERR: 2021-08-02T22:58:27.572959567Z with tarfile.TarFile(submission) as tar_ref: STDERR: 2021-08-02T22:58:27.572964286Z File "/usr/local/lib/python3.6/tarfile.py", line 1479, in __init__ STDERR: 2021-08-02T22:58:27.572966643Z self.firstmember = self.next() STDERR: 2021-08-02T22:58:27.572968757Z File "/usr/local/lib/python3.6/tarfile.py", line 2306, in next STDERR: 2021-08-02T22:58:27.572970960Z raise ReadError(str(e)) STDERR: 2021-08-02T22:58:27.572973080Z tarfile.ReadError: invalid header STDERR: 2021-08-02T22:58:27.572975197Z [job validate.cwl] Max memory used: 0MiB STDERR: 2021-08-02T22:58:27.572977314Z INFO:cwltool:[job validate.cwl] Max memory used: 0MiB STDERR: 2021-08-02T22:58:27.572979514Z [job validate.cwl] Job error: STDERR: 2021-08-02T22:58:27.572981707Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/validate.cwl:38:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-02T22:58:27.572984315Z ERROR:cwltool:[job validate.cwl] Job error: STDERR: 2021-08-02T22:58:27.572986528Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/validate.cwl:38:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-02T22:58:27.572989008Z [job validate.cwl] completed permanentFail STDERR: 2021-08-02T22:58:27.572991147Z WARNING:cwltool:[job validate.cwl] completed permanentFail STDERR: 2021-08-02T22:58:27.572993313Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:27.572995431Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-02T22:58:27.572997749Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-02T22:58:27.572999994Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-02T22:58:27.573002556Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-02T22:58:27.573004728Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-02T22:58:27.573006958Z return self.run(fileStore) STDERR: 2021-08-02T22:58:27.573009043Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-02T22:58:27.573011322Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-02T22:58:27.573013449Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-02T22:58:27.573016262Z ERROR:toil.worker:Exiting the worker because of a failed job on host 7f7c3083c323 STDERR: 2021-08-02T22:58:27.573020092Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m to 0 STDERR: 2021-08-02T22:58:27.573027662Z <========= STDERR: 2021-08-02T22:58:27.573628962Z 7f7c3083c323 2021-08-02 22:58:27,573 MainThread WARNING toil.leader: Job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m is completely failed STDERR: 2021-08-02T22:58:35.371143133Z 7f7c3083c323 2021-08-02 22:58:35,359 MainThread INFO toil.leader: Finished toil run with 4 failed jobs. STDERR: 2021-08-02T22:58:35.371176322Z 7f7c3083c323 2021-08-02 22:58:35,359 MainThread INFO toil.leader: Failed jobs at end of the run: '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-d5prkwgk '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-6o3cnmtr 'CWLWorkflow' kind-CWLWorkflow/instance-ojcce7b8 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m STDERR: 2021-08-02T22:58:35.385750502Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:35.385780101Z File "/usr/local/bin/toil-cwl-runner", line 8, in STDERR: 2021-08-02T22:58:35.385784589Z sys.exit(main()) STDERR: 2021-08-02T22:58:35.385787915Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 1691, in main STDERR: 2021-08-02T22:58:35.385792269Z outobj = toil.start(wf1) STDERR: 2021-08-02T22:58:35.385795665Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 829, in start STDERR: 2021-08-02T22:58:35.385799261Z return self._runMainLoop(rootJobGraph) STDERR: 2021-08-02T22:58:35.385802509Z File "/usr/local/lib/python3.6/site-packages/toil/common.py", line 1120, in _runMainLoop STDERR: 2021-08-02T22:58:35.385806021Z jobCache=self._jobCache).run() STDERR: 2021-08-02T22:58:35.385809121Z File "/usr/local/lib/python3.6/site-packages/toil/leader.py", line 269, in run STDERR: 2021-08-02T22:58:35.385812333Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2021-08-02T22:58:35.385815957Z toil.leader.FailedJobsException: The job store 'file:/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/tmp73s3ovmi' contains 4 failed jobs: '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-d5prkwgk, '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-6o3cnmtr, 'CWLWorkflow' kind-CWLWorkflow/instance-ojcce7b8, 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m STDERR: 2021-08-02T22:58:35.385848363Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m follows: STDERR: 2021-08-02T22:58:35.385852663Z =========> STDERR: 2021-08-02T22:58:35.385855750Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG--- STDERR: 2021-08-02T22:58:35.385859102Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe. STDERR: 2021-08-02T22:58:35.385862706Z [job validate.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-02T22:58:35.385866694Z WARNING:cwltool:[job validate.cwl] Skipping Docker software container '--memory' limit despite presence of ResourceRequirement with ramMin and/or ramMax setting. Consider running with --strict-memory-limit for increased portability assurance. STDERR: 2021-08-02T22:58:35.385870606Z [job validate.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk$ docker \ STDERR: 2021-08-02T22:58:35.385874534Z run \ STDERR: 2021-08-02T22:58:35.385877833Z -i \ STDERR: 2021-08-02T22:58:35.385880903Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk,target=/ZVUwcp \ STDERR: 2021-08-02T22:58:35.385885028Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_bw68fn6wm,target=/tmp \ STDERR: 2021-08-02T22:58:35.385889351Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmpigk4fjps.tmp,target=/var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991,readonly \ STDERR: 2021-08-02T22:58:35.385962010Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmplg34vtex.tmp,target=/var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T22:58:35.385971443Z --workdir=/ZVUwcp \ STDERR: 2021-08-02T22:58:35.385985802Z --read-only=true \ STDERR: 2021-08-02T22:58:35.385989001Z --user=0:0 \ STDERR: 2021-08-02T22:58:35.385992051Z --rm \ STDERR: 2021-08-02T22:58:35.385995151Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T22:58:35.385998387Z --env=HOME=/ZVUwcp \ STDERR: 2021-08-02T22:58:35.386001959Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_b_g3mmhte/20210802225826-255483.cid \ STDERR: 2021-08-02T22:58:35.386005776Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T22:58:35.386008961Z validate.py \ STDERR: 2021-08-02T22:58:35.386011983Z -p \ STDERR: 2021-08-02T22:58:35.386015107Z /var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991 \ STDERR: 2021-08-02T22:58:35.386018479Z -g \ STDERR: 2021-08-02T22:58:35.386021610Z /var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T22:58:35.386025003Z -e \ STDERR: 2021-08-02T22:58:35.386028050Z org.sagebionetworks.repo.model.FileEntity \ STDERR: 2021-08-02T22:58:35.386031216Z -o \ STDERR: 2021-08-02T22:58:35.386034187Z results.json STDERR: 2021-08-02T22:58:35.386037391Z INFO:cwltool:[job validate.cwl] /var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk$ docker \ STDERR: 2021-08-02T22:58:35.386041408Z run \ STDERR: 2021-08-02T22:58:35.386044455Z -i \ STDERR: 2021-08-02T22:58:35.386047660Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tqim0sjn7/tmp-out_27jx2sk,target=/ZVUwcp \ STDERR: 2021-08-02T22:58:35.386052028Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_bw68fn6wm,target=/tmp \ STDERR: 2021-08-02T22:58:35.386056862Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmpigk4fjps.tmp,target=/var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991,readonly \ STDERR: 2021-08-02T22:58:35.386061052Z --mount=type=bind,source=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tmplg34vtex.tmp,target=/var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip,readonly \ STDERR: 2021-08-02T22:58:35.386068036Z --workdir=/ZVUwcp \ STDERR: 2021-08-02T22:58:35.386071216Z --read-only=true \ STDERR: 2021-08-02T22:58:35.386074263Z --user=0:0 \ STDERR: 2021-08-02T22:58:35.386077340Z --rm \ STDERR: 2021-08-02T22:58:35.386080457Z --env=TMPDIR=/tmp \ STDERR: 2021-08-02T22:58:35.386083516Z --env=HOME=/ZVUwcp \ STDERR: 2021-08-02T22:58:35.386086645Z --cidfile=/var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/node-a86c9358-63f2-4a8f-aa76-8be9e1833f89-16349ee66b573b0d6cff3dbc6912349f/tmp1c5znrjt/5a008d17-33e5-4823-a380-8bee12cd04b1/tz3xvo7_b_g3mmhte/20210802225826-255483.cid \ STDERR: 2021-08-02T22:58:35.386090640Z docker.synapse.org/syn25829070/scoring:v2 \ STDERR: 2021-08-02T22:58:35.386093983Z validate.py \ STDERR: 2021-08-02T22:58:35.386097240Z -p \ STDERR: 2021-08-02T22:58:35.386100452Z /var/lib/cwl/stg1826ef54-854e-4d8a-9b15-f3e2584b4ad1/submission-9712991 \ STDERR: 2021-08-02T22:58:35.386103929Z -g \ STDERR: 2021-08-02T22:58:35.386107135Z /var/lib/cwl/stg98f6766d-ecca-495e-b195-fb0feed361f7/RSNA_ASNR_MICCAI_BraTS2021_ValidationGT.zip \ STDERR: 2021-08-02T22:58:35.386110617Z -e \ STDERR: 2021-08-02T22:58:35.386113730Z org.sagebionetworks.repo.model.FileEntity \ STDERR: 2021-08-02T22:58:35.386116844Z -o \ STDERR: 2021-08-02T22:58:35.386119821Z results.json STDERR: 2021-08-02T22:58:35.386122901Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:35.386126132Z File "/usr/local/lib/python3.6/tarfile.py", line 188, in nti STDERR: 2021-08-02T22:58:35.386129762Z s = nts(s, "ascii", "strict") STDERR: 2021-08-02T22:58:35.386135427Z File "/usr/local/lib/python3.6/tarfile.py", line 172, in nts STDERR: 2021-08-02T22:58:35.386138965Z return s.decode(encoding, errors) STDERR: 2021-08-02T22:58:35.386142213Z UnicodeDecodeError: 'ascii' codec can't decode byte 0xbc in position 1: ordinal not in range(128) STDERR: 2021-08-02T22:58:35.386145730Z STDERR: 2021-08-02T22:58:35.386149010Z During handling of the above exception, another exception occurred: STDERR: 2021-08-02T22:58:35.386152413Z STDERR: 2021-08-02T22:58:35.386155560Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:35.386158564Z File "/usr/local/lib/python3.6/tarfile.py", line 2294, in next STDERR: 2021-08-02T22:58:35.386162007Z tarinfo = self.tarinfo.fromtarfile(self) STDERR: 2021-08-02T22:58:35.386165020Z File "/usr/local/lib/python3.6/tarfile.py", line 1090, in fromtarfile STDERR: 2021-08-02T22:58:35.386204646Z obj = cls.frombuf(buf, tarfile.encoding, tarfile.errors) STDERR: 2021-08-02T22:58:35.386209120Z File "/usr/local/lib/python3.6/tarfile.py", line 1032, in frombuf STDERR: 2021-08-02T22:58:35.386216472Z chksum = nti(buf[148:156]) STDERR: 2021-08-02T22:58:35.386220031Z File "/usr/local/lib/python3.6/tarfile.py", line 191, in nti STDERR: 2021-08-02T22:58:35.386223364Z raise InvalidHeaderError("invalid header") STDERR: 2021-08-02T22:58:35.386226894Z tarfile.InvalidHeaderError: invalid header STDERR: 2021-08-02T22:58:35.386230263Z STDERR: 2021-08-02T22:58:35.386233443Z During handling of the above exception, another exception occurred: STDERR: 2021-08-02T22:58:35.386236826Z STDERR: 2021-08-02T22:58:35.386240076Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:35.386253978Z File "/usr/local/bin/validate.py", line 130, in STDERR: 2021-08-02T22:58:35.386257468Z main() STDERR: 2021-08-02T22:58:35.386260508Z File "/usr/local/bin/validate.py", line 108, in main STDERR: 2021-08-02T22:58:35.386263748Z preds = get_images(args.predictions_file) STDERR: 2021-08-02T22:58:35.386266886Z File "/usr/local/bin/validate.py", line 36, in get_images STDERR: 2021-08-02T22:58:35.386270219Z with tarfile.TarFile(submission) as tar_ref: STDERR: 2021-08-02T22:58:35.386273386Z File "/usr/local/lib/python3.6/tarfile.py", line 1479, in __init__ STDERR: 2021-08-02T22:58:35.386276788Z self.firstmember = self.next() STDERR: 2021-08-02T22:58:35.386280095Z File "/usr/local/lib/python3.6/tarfile.py", line 2306, in next STDERR: 2021-08-02T22:58:35.386283711Z raise ReadError(str(e)) STDERR: 2021-08-02T22:58:35.386286689Z tarfile.ReadError: invalid header STDERR: 2021-08-02T22:58:35.386290134Z [job validate.cwl] Max memory used: 0MiB STDERR: 2021-08-02T22:58:35.386293428Z INFO:cwltool:[job validate.cwl] Max memory used: 0MiB STDERR: 2021-08-02T22:58:35.386296742Z [job validate.cwl] Job error: STDERR: 2021-08-02T22:58:35.386299932Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/validate.cwl:38:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-02T22:58:35.386303744Z ERROR:cwltool:[job validate.cwl] Job error: STDERR: 2021-08-02T22:58:35.386306954Z ("Error collecting output for parameter 'results':\nbrats-dream-challenge-infra-main/validate.cwl:38:7: Did not find output file with glob pattern: '['results.json']'", {}) STDERR: 2021-08-02T22:58:35.386310585Z [job validate.cwl] completed permanentFail STDERR: 2021-08-02T22:58:35.386313718Z WARNING:cwltool:[job validate.cwl] completed permanentFail STDERR: 2021-08-02T22:58:35.386316919Z Traceback (most recent call last): STDERR: 2021-08-02T22:58:35.386320038Z File "/usr/local/lib/python3.6/site-packages/toil/worker.py", line 366, in workerScript STDERR: 2021-08-02T22:58:35.386323376Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer) STDERR: 2021-08-02T22:58:35.386326711Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1392, in _runner STDERR: 2021-08-02T22:58:35.386332858Z returnValues = self._run(jobGraph, fileStore) STDERR: 2021-08-02T22:58:35.386336164Z File "/usr/local/lib/python3.6/site-packages/toil/job.py", line 1329, in _run STDERR: 2021-08-02T22:58:35.386339506Z return self.run(fileStore) STDERR: 2021-08-02T22:58:35.386343184Z File "/usr/local/lib/python3.6/site-packages/toil/cwl/cwltoil.py", line 937, in run STDERR: 2021-08-02T22:58:35.386346676Z raise cwltool.errors.WorkflowException(status) STDERR: 2021-08-02T22:58:35.386349999Z cwltool.errors.WorkflowException: permanentFail STDERR: 2021-08-02T22:58:35.386353301Z ERROR:toil.worker:Exiting the worker because of a failed job on host 7f7c3083c323 STDERR: 2021-08-02T22:58:35.386356671Z WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/eda7095d-1091-464b-9749-1eaa47db3034/brats-dream-challenge-infra-main/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m with ID kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_eda7095d-1091-464b-9749-1eaa47db3034_brats-dream-challenge-infra-main_validate.cwl/instance-ghb6_x2m to 0 STDERR: 2021-08-02T22:58:35.386361551Z <========= " Could you kindly instruct how to do the process?