Created
May 11, 2024 13:29
-
-
Save ksuderman/4c173cbd86ceb8a698262df947cbd984 to your computer and use it in GitHub Desktop.
Pod details for failed SnpEff job
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| apiVersion: v1 | |
| kind: Pod | |
| metadata: | |
| name: gxy-galaxy-7sfwd-bcf7s | |
| generateName: gxy-galaxy-7sfwd- | |
| namespace: galaxy | |
| uid: 6d31be0a-146b-498a-82ad-1cd91f99d7ac | |
| resourceVersion: '77286' | |
| creationTimestamp: '2024-05-11T08:49:46Z' | |
| labels: | |
| app.galaxyproject.org/destination: k8s | |
| app.galaxyproject.org/handler: job_handler_0 | |
| app.galaxyproject.org/job_id: '30' | |
| app.kubernetes.io/component: tool | |
| app.kubernetes.io/instance: gxy-galaxy | |
| app.kubernetes.io/managed-by: galaxy | |
| app.kubernetes.io/name: snpEff | |
| app.kubernetes.io/part-of: galaxy | |
| app.kubernetes.io/version: 4.3_T.galaxy1 | |
| batch.kubernetes.io/controller-uid: 4d9602de-e371-45d6-ae16-477ba3efa1cd | |
| batch.kubernetes.io/job-name: gxy-galaxy-7sfwd | |
| controller-uid: 4d9602de-e371-45d6-ae16-477ba3efa1cd | |
| job-name: gxy-galaxy-7sfwd | |
| annotations: | |
| app.galaxyproject.org/tool_id: toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1 | |
| ownerReferences: | |
| - apiVersion: batch/v1 | |
| kind: Job | |
| name: gxy-galaxy-7sfwd | |
| uid: 4d9602de-e371-45d6-ae16-477ba3efa1cd | |
| controller: true | |
| blockOwnerDeletion: true | |
| managedFields: | |
| - manager: k3s | |
| operation: Update | |
| apiVersion: v1 | |
| time: '2024-05-11T08:49:46Z' | |
| fieldsType: FieldsV1 | |
| fieldsV1: | |
| f:metadata: | |
| f:annotations: | |
| .: {} | |
| f:app.galaxyproject.org/tool_id: {} | |
| f:generateName: {} | |
| f:labels: | |
| .: {} | |
| f:app.galaxyproject.org/destination: {} | |
| f:app.galaxyproject.org/handler: {} | |
| f:app.galaxyproject.org/job_id: {} | |
| f:app.kubernetes.io/component: {} | |
| f:app.kubernetes.io/instance: {} | |
| f:app.kubernetes.io/managed-by: {} | |
| f:app.kubernetes.io/name: {} | |
| f:app.kubernetes.io/part-of: {} | |
| f:app.kubernetes.io/version: {} | |
| f:batch.kubernetes.io/controller-uid: {} | |
| f:batch.kubernetes.io/job-name: {} | |
| f:controller-uid: {} | |
| f:job-name: {} | |
| f:ownerReferences: | |
| .: {} | |
| k:{"uid":"4d9602de-e371-45d6-ae16-477ba3efa1cd"}: {} | |
| f:spec: | |
| f:affinity: {} | |
| f:containers: | |
| k:{"name":"k8s"}: | |
| .: {} | |
| f:args: {} | |
| f:command: {} | |
| f:env: | |
| .: {} | |
| k:{"name":"GALAXY_MEMORY_MB"}: | |
| .: {} | |
| f:name: {} | |
| f:value: {} | |
| k:{"name":"GALAXY_MEMORY_MB_PER_SLOT"}: | |
| .: {} | |
| f:name: {} | |
| f:value: {} | |
| k:{"name":"GALAXY_SLOTS"}: | |
| .: {} | |
| f:name: {} | |
| f:value: {} | |
| f:image: {} | |
| f:imagePullPolicy: {} | |
| f:name: {} | |
| f:resources: | |
| .: {} | |
| f:limits: | |
| .: {} | |
| f:cpu: {} | |
| f:memory: {} | |
| f:requests: | |
| .: {} | |
| f:cpu: {} | |
| f:memory: {} | |
| f:terminationMessagePath: {} | |
| f:terminationMessagePolicy: {} | |
| f:volumeMounts: | |
| .: {} | |
| k:{"mountPath":"/cvmfs/cloud.galaxyproject.org"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:readOnly: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/cvmfs/data.galaxyproject.org"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:readOnly: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/config"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:readOnly: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/jobs_directory/000/30"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/objects/8/1/8"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/objects/c/6/7"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/objects/d/e/1/dataset_de135be2-5a00-48b2-8679-9d1c01655286.dat"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/objects/e/7/5/dataset_e75f0a1e-f8d2-4124-823f-7fccb29d18e4.dat"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/shed_tools"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:readOnly: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/tmp"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/tool-data"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:readOnly: {} | |
| f:subPath: {} | |
| k:{"mountPath":"/galaxy/server/database/tools"}: | |
| .: {} | |
| f:mountPath: {} | |
| f:name: {} | |
| f:readOnly: {} | |
| f:subPath: {} | |
| f:workingDir: {} | |
| f:dnsPolicy: {} | |
| f:enableServiceLinks: {} | |
| f:priorityClassName: {} | |
| f:restartPolicy: {} | |
| f:schedulerName: {} | |
| f:securityContext: | |
| .: {} | |
| f:fsGroup: {} | |
| f:supplementalGroups: {} | |
| f:terminationGracePeriodSeconds: {} | |
| f:volumes: | |
| .: {} | |
| k:{"name":"galaxy-galaxy-pvc"}: | |
| .: {} | |
| f:name: {} | |
| f:persistentVolumeClaim: | |
| .: {} | |
| f:claimName: {} | |
| k:{"name":"galaxy-refdata-gxy-pvc"}: | |
| .: {} | |
| f:name: {} | |
| f:persistentVolumeClaim: | |
| .: {} | |
| f:claimName: {} | |
| - manager: k3s | |
| operation: Update | |
| apiVersion: v1 | |
| time: '2024-05-11T08:49:58Z' | |
| fieldsType: FieldsV1 | |
| fieldsV1: | |
| f:status: | |
| f:conditions: | |
| k:{"type":"ContainersReady"}: | |
| .: {} | |
| f:lastProbeTime: {} | |
| f:lastTransitionTime: {} | |
| f:reason: {} | |
| f:status: {} | |
| f:type: {} | |
| k:{"type":"Initialized"}: | |
| .: {} | |
| f:lastProbeTime: {} | |
| f:lastTransitionTime: {} | |
| f:status: {} | |
| f:type: {} | |
| k:{"type":"Ready"}: | |
| .: {} | |
| f:lastProbeTime: {} | |
| f:lastTransitionTime: {} | |
| f:reason: {} | |
| f:status: {} | |
| f:type: {} | |
| f:containerStatuses: {} | |
| f:hostIP: {} | |
| f:phase: {} | |
| f:podIP: {} | |
| f:podIPs: | |
| .: {} | |
| k:{"ip":"10.42.0.58"}: | |
| .: {} | |
| f:ip: {} | |
| f:startTime: {} | |
| subresource: status | |
| selfLink: /api/v1/namespaces/galaxy/pods/gxy-galaxy-7sfwd-bcf7s | |
| status: | |
| phase: Failed | |
| conditions: | |
| - type: Initialized | |
| status: 'True' | |
| lastProbeTime: null | |
| lastTransitionTime: '2024-05-11T08:49:46Z' | |
| - type: Ready | |
| status: 'False' | |
| lastProbeTime: null | |
| lastTransitionTime: '2024-05-11T08:49:56Z' | |
| reason: PodFailed | |
| - type: ContainersReady | |
| status: 'False' | |
| lastProbeTime: null | |
| lastTransitionTime: '2024-05-11T08:49:56Z' | |
| reason: PodFailed | |
| - type: PodScheduled | |
| status: 'True' | |
| lastProbeTime: null | |
| lastTransitionTime: '2024-05-11T08:49:46Z' | |
| hostIP: 10.142.0.40 | |
| podIP: 10.42.0.58 | |
| podIPs: | |
| - ip: 10.42.0.58 | |
| startTime: '2024-05-11T08:49:46Z' | |
| containerStatuses: | |
| - name: k8s | |
| state: | |
| terminated: | |
| exitCode: 255 | |
| reason: Error | |
| startedAt: '2024-05-11T08:49:52Z' | |
| finishedAt: '2024-05-11T08:49:55Z' | |
| containerID: >- | |
| containerd://1c1b9ea27e339d5ac16fa27a41060dff804adf5350c5c77c2fc67851918e2e65 | |
| lastState: {} | |
| ready: false | |
| restartCount: 0 | |
| image: quay.io/biocontainers/snpeff:4.3.1t--hdfd78af_5 | |
| imageID: >- | |
| quay.io/biocontainers/snpeff@sha256:4dc783ccbf4da1332f3935f19fc98b66244f5c47b3f9a87a5b86515f97bd44d9 | |
| containerID: >- | |
| containerd://1c1b9ea27e339d5ac16fa27a41060dff804adf5350c5c77c2fc67851918e2e65 | |
| started: false | |
| qosClass: Guaranteed | |
| spec: | |
| volumes: | |
| - name: galaxy-refdata-gxy-pvc | |
| persistentVolumeClaim: | |
| claimName: galaxy-refdata-gxy-pvc | |
| - name: galaxy-galaxy-pvc | |
| persistentVolumeClaim: | |
| claimName: galaxy-galaxy-pvc | |
| - name: kube-api-access-srm29 | |
| projected: | |
| sources: | |
| - serviceAccountToken: | |
| expirationSeconds: 3607 | |
| path: token | |
| - configMap: | |
| name: kube-root-ca.crt | |
| items: | |
| - key: ca.crt | |
| path: ca.crt | |
| - downwardAPI: | |
| items: | |
| - path: namespace | |
| fieldRef: | |
| apiVersion: v1 | |
| fieldPath: metadata.namespace | |
| defaultMode: 420 | |
| containers: | |
| - name: k8s | |
| image: quay.io/biocontainers/snpeff:4.3.1t--hdfd78af_5 | |
| command: | |
| - /bin/bash | |
| args: | |
| - '-c' | |
| - >- | |
| /galaxy/server/database/jobs_directory/000/30/galaxy_30.sh; exit $(cat | |
| /galaxy/server/database/jobs_directory/000/30/galaxy_30.ec) | |
| workingDir: /galaxy/server/database/jobs_directory/000/30 | |
| env: | |
| - name: GALAXY_SLOTS | |
| value: '1' | |
| - name: GALAXY_MEMORY_MB | |
| value: '12884' | |
| - name: GALAXY_MEMORY_MB_PER_SLOT | |
| value: '12884' | |
| resources: | |
| limits: | |
| cpu: '1' | |
| memory: '12884901888' | |
| requests: | |
| cpu: '1' | |
| memory: '12884901888' | |
| volumeMounts: | |
| - name: galaxy-galaxy-pvc | |
| mountPath: >- | |
| /galaxy/server/database/objects/d/e/1/dataset_de135be2-5a00-48b2-8679-9d1c01655286.dat | |
| subPath: objects/d/e/1/dataset_de135be2-5a00-48b2-8679-9d1c01655286.dat | |
| - name: galaxy-galaxy-pvc | |
| mountPath: >- | |
| /galaxy/server/database/objects/e/7/5/dataset_e75f0a1e-f8d2-4124-823f-7fccb29d18e4.dat | |
| subPath: objects/e/7/5/dataset_e75f0a1e-f8d2-4124-823f-7fccb29d18e4.dat | |
| - name: galaxy-galaxy-pvc | |
| mountPath: /galaxy/server/database/objects/c/6/7 | |
| subPath: objects/c/6/7 | |
| - name: galaxy-galaxy-pvc | |
| mountPath: /galaxy/server/database/objects/8/1/8 | |
| subPath: objects/8/1/8 | |
| - name: galaxy-galaxy-pvc | |
| mountPath: /galaxy/server/database/jobs_directory/000/30 | |
| subPath: jobs_directory/000/30 | |
| - name: galaxy-galaxy-pvc | |
| readOnly: true | |
| mountPath: /galaxy/server/database/config | |
| subPath: config | |
| - name: galaxy-galaxy-pvc | |
| mountPath: /galaxy/server/database/tmp | |
| subPath: tmp | |
| - name: galaxy-galaxy-pvc | |
| readOnly: true | |
| mountPath: /galaxy/server/database/tool-data | |
| subPath: tool-data | |
| - name: galaxy-galaxy-pvc | |
| readOnly: true | |
| mountPath: /galaxy/server/database/tools | |
| subPath: tools | |
| - name: galaxy-galaxy-pvc | |
| readOnly: true | |
| mountPath: /galaxy/server/database/shed_tools | |
| subPath: shed_tools | |
| - name: galaxy-refdata-gxy-pvc | |
| readOnly: true | |
| mountPath: /cvmfs/data.galaxyproject.org | |
| subPath: data.galaxyproject.org | |
| - name: galaxy-galaxy-pvc | |
| readOnly: true | |
| mountPath: /cvmfs/cloud.galaxyproject.org | |
| subPath: cvmfsclone | |
| - name: kube-api-access-srm29 | |
| readOnly: true | |
| mountPath: /var/run/secrets/kubernetes.io/serviceaccount | |
| terminationMessagePath: /dev/termination-log | |
| terminationMessagePolicy: File | |
| imagePullPolicy: IfNotPresent | |
| restartPolicy: Never | |
| terminationGracePeriodSeconds: 30 | |
| dnsPolicy: ClusterFirst | |
| serviceAccountName: default | |
| serviceAccount: default | |
| nodeName: ks-dev | |
| securityContext: | |
| supplementalGroups: | |
| - 101 | |
| fsGroup: 101 | |
| affinity: {} | |
| schedulerName: default-scheduler | |
| tolerations: | |
| - key: node.kubernetes.io/not-ready | |
| operator: Exists | |
| effect: NoExecute | |
| tolerationSeconds: 300 | |
| - key: node.kubernetes.io/unreachable | |
| operator: Exists | |
| effect: NoExecute | |
| tolerationSeconds: 300 | |
| priorityClassName: galaxy-job-priority | |
| priority: -1000 | |
| enableServiceLinks: true | |
| preemptionPolicy: Never |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment