使用 的 HealthOmics 範例 AWS CLI

若要停止分段讀取集合上傳

下列abort-multipart-read-set-upload範例會停止分段讀取集上傳至您的 HealthOmics 序列存放區。

aws omics abort-multipart-read-set-upload \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455

此命令不會產生輸出。

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的直接上傳至序列存放區。

若要接受分析存放區資料的共用

下列accept-share範例接受 HealthOmics 分析存放區資料的共用。

aws omics accept-share \
    ----share-id "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a"

輸出：

{
    "status": "ACTIVATING"
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的跨帳戶共用。

若要刪除多個讀取集合

下列batch-delete-read-set範例會刪除兩個讀取集。

aws omics batch-delete-read-set \
    --sequence-store-id 1234567890 \
    --ids 1234567890 0123456789

如果刪除任何指定的讀取集時發生錯誤，服務會傳回錯誤清單。

{
    "errors": [
        {
            "code": "",
            "id": "0123456789",
            "message": "The specified readset does not exist."
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要取消註釋匯入任務

下列cancel-annotation-import-job範例會取消 ID 為 的註釋匯入任務04f57618-xmpl-4fd0-9349-e5a85aefb997。

aws omics cancel-annotation-import-job \
    --job-id 04f57618-xmpl-4fd0-9349-e5a85aefb997

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

若要取消執行

下列cancel-run範例會取消 ID 為 的執行1234567。

aws omics cancel-run \
    --id 1234567

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要取消變體匯入任務

下列cancel-variant-import-job範例會取消 ID 為 的變體匯入任務69cb65d6-xmpl-4a4a-9025-4565794b684e。

aws omics cancel-variant-import-job \
    --job-id 69cb65d6-xmpl-4a4a-9025-4565794b684e

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

上傳所有元件後，完成分段上傳。

所有元件上傳完成後，下列complete-multipart-read-set-upload範例會結束分段上傳至序列存放區。

aws omics complete-multipart-read-set-upload \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455 \
    --parts '[{"checksum":"gaCBQMe+rpCFZxLpoP6gydBoXaKKDA/Vobh5zBDb4W4=","partNumber":1,"partSource":"SOURCE1"}]'

輸出：

{
    "readSetId": "0000000001"
    "readSetId": "0000000002"
    "readSetId": "0000000003"
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的直接上傳至序列存放區。

建立新的註釋存放區版本

下列create-annotation-store-version範例會建立新的註釋存放區版本。

aws omics create-annotation-store-version \
    --name my_annotation_store \
    --version-name my_version

輸出：

{
    "creationTime": "2023-07-21T17:15:49.251040+00:00",
    "id": "3b93cdef69d2",
    "name": "my_annotation_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:555555555555:referenceStore/6505293348/reference/5987565360"
    },
    "status": "CREATING",
    "versionName": "my_version"
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的建立新版本的註釋存放區。

範例 1：建立 VCF 註釋存放區

下列create-annotation-store範例會建立 VCF 格式註釋存放區。

aws omics create-annotation-store \
    --name my_ann_store \
    --store-format VCF \
    --reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890

輸出：

{
    "creationTime": "2022-11-23T22:48:39.226492Z",
    "id": "0a91xmplc71f",
    "name": "my_ann_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeFormat": "VCF"
}

範例 2：建立 TSV 註釋存放區

下列create-annotation-store範例會建立 TSV 格式註釋存放區。

aws omics create-annotation-store \
    --name tsv_ann_store \
    --store-format TSV \
    --reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890 \
    --store-options file://tsv-store-options.json

tsv-store-options.json 設定註釋的格式選項。

{
    "tsvStoreOptions": {
        "annotationType": "CHR_START_END_ZERO_BASE",
        "formatToHeader": {
            "CHR": "chromosome",
            "START": "start",
            "END": "end"
        },
        "schema": [
            {
                "chromosome": "STRING"
            },
            {
                "start": "LONG"
            },
            {
                "end": "LONG"
            },
            {
                "name": "STRING"
            }
        ]
    }
}

輸出：

{
    "creationTime": "2022-11-30T01:28:08.525586Z",
    "id": "861cxmpl96b0",
    "name": "tsv_ann_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeFormat": "TSV",
    "storeOptions": {
        "tsvStoreOptions": {
            "annotationType": "CHR_START_END_ZERO_BASE",
            "formatToHeader": {
                "CHR": "chromosome",
                "END": "end",
                "START": "start"
            },
            "schema": [
                {
                    "chromosome": "STRING"
                },
                {
                    "start": "LONG"
                },
                {
                    "end": "LONG"
                },
                {
                    "name": "STRING"
                }
            ]
        }
    }
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

開始分段讀取集上傳。

下列create-multipart-read-set-upload範例會啟動分段讀取集合上傳。

aws omics create-multipart-read-set-upload \
    --sequence-store-id 0123456789 \
    --name HG00146 \
    --source-file-type FASTQ \
    --subject-id mySubject\
    --sample-id mySample\
    --description "FASTQ for HG00146"\
    --generated-from "1000 Genomes"

輸出：

{
    "creationTime": "2022-07-13T23:25:20Z",
    "description": "FASTQ for HG00146",
    "generatedFrom": "1000 Genomes",
    "name": "HG00146",
    "sampleId": "mySample",
    "sequenceStoreId": "0123456789",
    "sourceFileType": "FASTQ",
    "subjectId": "mySubject",
    "uploadId": "1122334455"
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的直接上傳至序列存放區。

建立參考存放區

下列create-reference-store範例會建立參考存放區 my-ref-store。

aws omics create-reference-store \
    --name my-ref-store

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890",
    "creationTime": "2022-11-22T22:13:25.947Z",
    "id": "1234567890",
    "name": "my-ref-store"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

建立執行群組

下列create-run-group範例會建立名為 的執行群組cram-converter。

aws omics create-run-group \
    --name cram-converter \
    --max-cpus 20 \
    --max-duration 600

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
    "id": "1234567",
    "tags": {}
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

建立序列存放區

下列create-sequence-store範例會建立序列存放區。

aws omics create-sequence-store \
    --name my-seq-store

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890",
    "creationTime": "2022-11-23T01:24:33.629Z",
    "id": "1234567890",
    "name": "my-seq-store"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

建立 a HealthOmics 分析存放區的共用

下列create-share範例示範如何建立 a HealthOmics 分析存放區的共用，可由帳戶外部的訂閱者接受。

aws omics create-share \
    --resource-arn "arn:aws:omics:us-west-2:555555555555:variantStore/omics_dev_var_store" \
    --principal-subscriber "123456789012" \
    --name "my_Share-123"

輸出：

{
    "shareId": "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a",
    "name": "my_Share-123",
    "status": "PENDING"
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的跨帳戶共用。

若要建立變體存放區

下列create-variant-store範例會建立名為 的變體存放區my_var_store。

aws omics create-variant-store \
    --name my_var_store \
    --reference referenceArn=arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890

輸出：

{
    "creationTime": "2022-11-23T22:09:07.534499Z",
    "id": "02dexmplcfdd",
    "name": "my_var_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

建立工作流程

下列create-workflow範例會建立 WDL 工作流程。

aws omics create-workflow \
    --name cram-converter \
    --engine WDL \
    --definition-zip fileb://workflow-crambam.zip \
    --parameter-template file://workflow-params.json

workflow-crambam.zip 是包含工作流程定義的 ZIP 封存。 workflow-params.json 定義工作流程的執行期參數。

{
    "ref_fasta" : {
        "description": "Reference genome fasta file",
        "optional": false
    },
    "ref_fasta_index" : {
        "description": "Index of the reference genome fasta file",
        "optional": false
    },
    "ref_dict" : {
        "description": "dictionary file for 'ref_fasta'",
        "optional": false
    },
    "input_cram" : {
        "description": "The Cram file to convert to BAM",
        "optional": false
    },
    "sample_name" : {
        "description": "The name of the input sample, used to name the output BAM",
        "optional": false
    }
}

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
    "id": "1234567",
    "status": "CREATING",
    "tags": {}
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要刪除註釋存放區版本

下列delete-annotation-store-versions範例會刪除註釋存放區版本。

aws omics delete-annotation-store-versions \
    --name my_annotation_store \
    --versions my_version

輸出：

{
    "errors": []
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的建立新版本的註釋存放區。

若要刪除註釋存放區

下列delete-annotation-store範例會刪除名為 的註釋存放區my_vcf_store。

aws omics delete-annotation-store \
    --name my_vcf_store

輸出：

{
    "status": "DELETING"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

若要刪除參考存放區

下列delete-reference-store範例會刪除 ID 為 的參考存放區1234567890。

aws omics delete-reference-store \
    --id 1234567890

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要刪除參考

下列delete-reference範例會刪除參考。

aws omics delete-reference \
    --reference-store-id 1234567890 \
    --id 1234567890

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

刪除執行群組

下列delete-run-group範例會刪除 ID 為 的執行群組1234567。

aws omics delete-run-group \
    --id 1234567

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

刪除工作流程執行

下列delete-run範例會刪除 ID 為 的執行1234567。

aws omics delete-run \
    --id 1234567

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要刪除序列存放區

下列delete-sequence-store範例會刪除 ID 為 的序列存放區1234567890。

aws omics delete-sequence-store \
    --id 1234567890

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

刪除 HealthOmics 分析資料的共用

下列delete-share範例會刪除分析資料的跨帳戶共用。

aws omics delete-share \
    --share-id "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a"

輸出：

{
    "status": "DELETING"
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的跨帳戶共用。

若要刪除變體存放區

下列delete-variant-store範例會刪除名為 的變體存放區my_var_store。

aws omics delete-variant-store \
    --name my_var_store

輸出：

{
    "status": "DELETING"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

刪除工作流程

下列delete-workflow範例會刪除 ID 為 的工作流程1234567。

aws omics delete-workflow \
    --id 1234567

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

檢視註釋匯入任務

下列get-annotation-import-job範例會取得註釋匯入工作的詳細資訊。

aws omics get-annotation-import-job \
    --job-id 984162c7-xmpl-4d23-ab47-286f7950bfbf

輸出：

{
    "creationTime": "2022-11-30T01:40:11.017746Z",
    "destinationName": "tsv_ann_store",
    "id": "984162c7-xmpl-4d23-ab47-286f7950bfbf",
    "items": [
        {
            "jobStatus": "COMPLETED",
            "source": "s3://omics-artifacts-01d6xmpl4e72dd32/targetedregions.bed.gz"
        }
    ],
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "runLeftNormalization": false,
    "status": "COMPLETED",
    "updateTime": "2022-11-30T01:42:39.134009Z"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

若要擷取註釋存放區版本的中繼資料

下列get-annotation-store-version範例會擷取所請求註釋存放區版本的中繼資料。

aws omics get-annotation-store-version \
    --name my_annotation_store \
    --version-name my_version

輸出：

{
    "storeId": "4934045d1c6d",
    "id": "2a3f4a44aa7b",
    "status": "ACTIVE",
    "versionArn": "arn:aws:omics:us-west-2:555555555555:annotationStore/my_annotation_store/version/my_version",
    "name": "my_annotation_store",
    "versionName": "my_version",
    "creationTime": "2023-07-21T17:15:49.251040+00:00",
    "updateTime": "2023-07-21T17:15:56.434223+00:00",
    "statusMessage": "",
    "versionSizeBytes": 0
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的建立新版本的註釋存放區。

檢視註釋存放區

下列get-annotation-store範例會取得名為 的註釋存放區詳細資訊my_ann_store。

aws omics get-annotation-store \
    --name my_ann_store

輸出：

{
    "creationTime": "2022-11-23T22:48:39.226492Z",
    "id": "0a91xmplc71f",
    "name": "my_ann_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeArn": "arn:aws:omics:us-west-2:123456789012:annotationStore/my_ann_store",
    "storeFormat": "VCF",
    "storeSizeBytes": 0,
    "tags": {}
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

檢視讀取集啟用任務

下列get-read-set-activation-job範例會取得讀取集啟用工作的詳細資訊。

aws omics get-read-set-activation-job \
    --sequence-store-id 1234567890 \
    --id 1234567890

輸出：

{
    "completionTime": "2022-12-06T22:33:42.828Z",
    "creationTime": "2022-12-06T22:32:45.213Z",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "sources": [
        {
            "readSetId": "1234567890",
            "status": "FINISHED",
            "statusMessage": "No activation needed as read set is already in ACTIVATING or ACTIVE state."
        }
    ],
    "status": "COMPLETED",
    "statusMessage": "The job completed successfully."
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

檢視讀取集匯出任務

下列get-read-set-export-job範例會取得讀取集匯出工作的詳細資訊。

aws omics get-read-set-export-job \
    --sequence-store-id 1234567890 \
    --id 1234567890

輸出：

{
    "completionTime": "2022-12-06T22:39:14.491Z",
    "creationTime": "2022-12-06T22:37:18.612Z",
    "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "status": "COMPLETED",
    "statusMessage": "The job is submitted and will start soon."
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

檢視讀取集匯入任務

下列get-read-set-import-job範例會取得讀取集匯入工作的詳細資訊。

aws omics get-read-set-import-job \
    --sequence-store-id 1234567890 \
    --id 1234567890

輸出：

{
    "creationTime": "2022-11-23T01:36:38.158Z",
    "id": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "sequenceStoreId": "1234567890",
    "sources": [
        {
            "name": "HG00100",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "bam-sample",
            "sourceFileType": "BAM",
            "sourceFiles": {
                "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam",
                "source2": ""
            },
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress.",
            "subjectId": "bam-subject",
            "tags": {
                "aws:omics:sampleId": "bam-sample",
                "aws:omics:subjectId": "bam-subject"
            }
        },
        {
            "name": "HG00146",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "fastq-sample",
            "sourceFileType": "FASTQ",
            "sourceFiles": {
                "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/SRR233106_1.filt.fastq.gz",
                "source2": "s3://omics-artifacts-01d6xmpl4e72dd32/SRR233106_2.filt.fastq.gz"
            },
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress.",
            "subjectId": "fastq-subject",
            "tags": {
                "aws:omics:sampleId": "fastq-sample",
                "aws:omics:subjectId": "fastq-subject"
            }
        },
        {
            "name": "HG00096",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "cram-sample",
            "sourceFileType": "CRAM",
            "sourceFiles": {
                "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/HG00096.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram",
                "source2": ""
            },
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress.",
            "subjectId": "cram-subject",
            "tags": {
                "aws:omics:sampleId": "cram-sample",
                "aws:omics:subjectId": "cram-subject"
            }
        }
    ],
    "status": "IN_PROGRESS",
    "statusMessage": "The job is currently in progress."
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

檢視讀取集合

下列get-read-set-metadata範例會取得讀取集檔案的詳細資訊。

aws omics get-read-set-metadata \
    --sequence-store-id 1234567890 \
    --id 1234567890

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890/readSet/1234567890",
    "creationTime": "2022-11-23T21:55:00.515Z",
    "fileType": "FASTQ",
    "files": {
        "source1": {
            "contentLength": 310054739,
            "partSize": 104857600,
            "totalParts": 3
        },
        "source2": {
            "contentLength": 307846621,
            "partSize": 104857600,
            "totalParts": 3
        }
    },
    "id": "1234567890",
    "name": "HG00146",
    "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
    "sampleId": "fastq-sample",
    "sequenceInformation": {
        "alignment": "UNALIGNED",
        "totalBaseCount": 677717384,
        "totalReadCount": 8917334
    },
    "sequenceStoreId": "1234567890",
    "status": "ACTIVE",
    "subjectId": "fastq-subject"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

下載讀取集

下列get-read-set範例會將讀取集的第 3 部分下載為 1234567890.3.bam。

aws omics get-read-set \
    --sequence-store-id 1234567890 \
    --id 1234567890 \
    --part-number 3  1234567890.3.bam

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

檢視參考匯入任務

下列get-reference-import-job範例會取得參考匯入任務的詳細資訊。

aws omics get-reference-import-job \
    --reference-store-id 1234567890 \
    --id 1234567890

輸出：

{
    "creationTime": "2022-11-22T22:25:41.124Z",
    "id": "1234567890",
    "referenceStoreId": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "sources": [
        {
            "name": "assembly-38",
            "sourceFile": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta",
            "status": "IN_PROGRESS",
            "statusMessage": "The source job is currently in progress."
        }
    ],
    "status": "IN_PROGRESS",
    "statusMessage": "The job is currently in progress."
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

檢視參考

下列get-reference-metadata範例會取得參考的詳細資訊。

aws omics get-reference-metadata \
    --reference-store-id 1234567890 \
    --id 1234567890

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
    "creationTime": "2022-11-22T22:27:09.033Z",
    "files": {
        "index": {
            "contentLength": 160928,
            "partSize": 104857600,
            "totalParts": 1
        },
        "source": {
            "contentLength": 3249912778,
            "partSize": 104857600,
            "totalParts": 31
        }
    },
    "id": "1234567890",
    "md5": "7ff134953dcca8c8997453bbb80b6b5e",
    "name": "assembly-38",
    "referenceStoreId": "1234567890",
    "status": "ACTIVE",
    "updateTime": "2022-11-22T22:27:09.033Z"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

檢視參考存放區

下列get-reference-store範例會取得參考存放區的詳細資訊。

aws omics get-reference-store \
    --id 1234567890

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890",
    "creationTime": "2022-09-23T23:27:20.364Z",
    "id": "1234567890",
    "name": "my-rstore-0"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要下載基因體參考

下列get-reference範例會將基因體的第 1 部分下載為 hg38.1.fa。

aws omics get-reference \
    --reference-store-id 1234567890 \
    --id 1234567890 \
    --part-number 1 hg38.1.fa

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

檢視執行群組

下列get-run-group範例會取得執行群組的詳細資訊。

aws omics get-run-group \
    --id 1234567

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
    "creationTime": "2022-12-01T00:58:42.915219Z",
    "id": "1234567",
    "maxCpus": 20,
    "maxDuration": 600,
    "name": "cram-convert",
    "tags": {}
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

檢視任務

下列get-run-task範例會取得工作流程任務的詳細資訊。

aws omics get-run-task \
    --id 1234567 \
    --task-id 1234567

輸出：

{
    "cpus": 1,
    "creationTime": "2022-11-30T23:13:00.718651Z",
    "logStream": "arn:aws:logs:us-west-2:123456789012:log-group:/aws/omics/WorkflowLog:log-stream:run/1234567/task/1234567",
    "memory": 15,
    "name": "CramToBamTask",
    "startTime": "2022-11-30T23:17:47.016Z",
    "status": "COMPLETED",
    "stopTime": "2022-11-30T23:18:21.503Z",
    "taskId": "1234567"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

檢視工作流程執行

下列get-run範例會取得工作流程執行的詳細資訊。

aws omics get-run \
    --id 1234567

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
    "creationTime": "2022-11-30T22:58:22.615865Z",
    "digest": "sha256:c54bxmpl742dcc26f7fa1f10e37550ddd8f251f418277c0a58e895b801ed28cf",
    "id": "1234567",
    "name": "cram-to-bam",
    "outputUri": "s3://omics-artifacts-01d6xmpl4e72dd32/workflow-output/",
    "parameters": {
        "ref_dict": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict",
        "ref_fasta_index": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta.fai",
        "ref_fasta": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta",
        "sample_name": "NA12878",
        "input_cram": "s3://omics-artifacts-01d6xmpl4e72dd32/NA12878.cram"
    },
    "resourceDigests": {
        "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta.fai": "etag:f76371b113734a56cde236bc0372de0a",
        "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict": "etag:3884c62eb0e53fa92459ed9bff133ae6",
        "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta": "etag:e307d81c605fb91b7720a08f00276842-388",
        "s3://omics-artifacts-01d6xmpl4e72dd32/NA12878.cram": "etag:a9f52976381286c6143b5cc681671ec6"
    },
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "startedBy": "arn:aws:iam::123456789012:user/laptop-2020",
    "status": "STARTING",
    "tags": {},
    "workflowId": "1234567",
    "workflowType": "PRIVATE"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

檢視序列存放區

下列get-sequence-store範例取得 ID 為 的序列存放區詳細資訊1234567890。

aws omics get-sequence-store \
    --id 1234567890

輸出：

{
    "arn": "arn:aws:omics:us-east-1:123456789012:sequenceStore/1234567890",
    "creationTime": "2022-11-23T19:55:48.376Z",
    "id": "1234567890",
    "name": "my-seq-store"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

擷取有關 a HealthOmics 分析資料共用的中繼資料

下列get-share範例會擷取分析資料跨帳戶共用的中繼資料。

aws omics get-share \
    --share-id "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a"

輸出：

{
    "share": {
        "shareId": "495c21bedc889d07d0ab69d710a6841e-dd75ab7a1a9c384fa848b5bd8e5a7e0a",
        "name": "my_Share-123",
        "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/omics_dev_var_store",
        "principalSubscriber": "123456789012",
        "ownerId": "555555555555",
        "status": "PENDING"
    }
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的跨帳戶共用。

檢視變體匯入任務

下列get-variant-import-job範例會取得變體匯入任務的詳細資訊。

aws omics get-variant-import-job \
    --job-id edd7b8ce-xmpl-47e2-bc99-258cac95a508

輸出：

{
    "creationTime": "2022-11-23T22:42:50.037812Z",
    "destinationName": "my_var_store",
    "id": "edd7b8ce-xmpl-47e2-bc99-258cac95a508",
    "items": [
        {
            "jobStatus": "IN_PROGRESS",
            "source": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.known_indels.vcf.gz"
        }
    ],
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "runLeftNormalization": false,
    "status": "IN_PROGRESS",
    "updateTime": "2022-11-23T22:43:05.898309Z"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

檢視變體存放區

下列get-variant-store範例會取得變體存放區的詳細資訊。

aws omics get-variant-store \
    --name my_var_store

輸出：

{
    "creationTime": "2022-11-23T22:09:07.534499Z",
    "id": "02dexmplcfdd",
    "name": "my_var_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "CREATING",
    "storeArn": "arn:aws:omics:us-west-2:123456789012:variantStore/my_var_store",
    "storeSizeBytes": 0,
    "tags": {},
    "updateTime": "2022-11-23T22:09:24.931711Z"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

檢視工作流程

下列get-workflow範例取得 ID 為 之工作流程的詳細資訊1234567。

aws omics get-workflow \
    --id 1234567

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
    "creationTime": "2022-11-30T22:33:16.225368Z",
    "digest": "sha256:c54bxmpl742dcc26f7fa1f10e37550ddd8f251f418277c0a58e895b801ed28cf",
    "engine": "WDL",
    "id": "1234567",
    "main": "workflow-crambam.wdl",
    "name": "cram-converter",
    "parameterTemplate": {
        "ref_dict": {
            "description": "dictionary file for 'ref_fasta'"
        },
        "ref_fasta_index": {
            "description": "Index of the reference genome fasta file"
        },
        "ref_fasta": {
            "description": "Reference genome fasta file"
        },
        "input_cram": {
            "description": "The Cram file to convert to BAM"
        },
        "sample_name": {
            "description": "The name of the input sample, used to name the output BAM"
        }
    },
    "status": "ACTIVE",
    "statusMessage": "workflow-crambam.wdl\n    workflow CramToBamFlow\n        call CramToBamTask\n        call ValidateSamFile\n    task CramToBamTask\n    task ValidateSamFile\n",
    "tags": {},
    "type": "PRIVATE"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要取得註釋匯入任務的清單

以下內容list-annotation-import-jobs會取得註釋匯入任務的清單。

aws omics list-annotation-import-jobs

輸出：

{
    "annotationImportJobs": [
        {
            "creationTime": "2022-11-30T01:39:41.478294Z",
            "destinationName": "gff_ann_store",
            "id": "18a9e792-xmpl-4869-a105-e5b602900444",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "COMPLETED",
            "updateTime": "2022-11-30T01:47:09.145178Z"
        },
        {
            "creationTime": "2022-11-30T00:45:58.007838Z",
            "destinationName": "my_ann_store",
            "id": "4e9eafc8-xmpl-431e-a0b2-3bda27cb600a",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "FAILED",
            "updateTime": "2022-11-30T00:47:01.706325Z"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

列出註釋存放區的所有版本。

下列list-annotation-store-versions範例會列出註釋存放區中存在的所有版本。

aws omics list-annotation-store-versions \
    --name my_annotation_store

輸出：

{
    "annotationStoreVersions": [
        {
        "storeId": "4934045d1c6d",
        "id": "2a3f4a44aa7b",
        "status": "CREATING",
        "versionArn": "arn:aws:omics:us-west-2:555555555555:annotationStore/my_annotation_store/version/my_version_2",
        "name": "my_annotation_store",
        "versionName": "my_version_2",
        "creation Time": "2023-07-21T17:20:59.380043+00:00",
        "versionSizeBytes": 0
},
{
     "storeId": "4934045d1c6d",
     "id": "4934045d1c6d",
     "status": "ACTIVE",
     "versionArn": "arn:aws:omics:us-west-2:555555555555:annotationStore/my_annotation_store/version/my_version_1",
     "name": "my_annotation_store",
     "versionName": "my_version_1",
     "creationTime": "2023-07-21T17:15:49.251040+00:00",
     "updateTime": "2023-07-21T17:15:56.434223+00:00",
     "statusMessage": "",
     "versionSizeBytes": 0
     }

}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的建立新版本的註釋存放區。

若要取得註釋存放區的清單

下列list-annotation-stores範例會取得註釋存放區的清單。

aws omics list-annotation-stores

輸出：

{
    "annotationStores": [
        {
            "creationTime": "2022-11-23T22:48:39.226492Z",
            "id": "0a91xmplc71f",
            "name": "my_ann_store",
            "reference": {
                "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
            },
            "status": "ACTIVE",
            "statusMessage": "",
            "storeArn": "arn:aws:omics:us-west-2:123456789012:annotationStore/my_ann_store",
            "storeFormat": "VCF",
            "storeSizeBytes": 0,
            "updateTime": "2022-11-23T22:53:27.372840Z"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

列出所有分段讀取集合上傳及其狀態。

下列list-multipart-read-set-uploads範例會列出所有分段讀取集合上傳及其狀態。

aws omics list-multipart-read-set-uploads \
    --sequence-store-id 0123456789

輸出：

{
"uploads":
    [
        {
           "sequenceStoreId": "0123456789",
           "uploadId": "8749584421",
           "sourceFileType": "FASTQ",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "name": "HG00146",
            "description": "FASTQ for HG00146",
            "creationTime": "2023-11-29T19:22:51.349298+00:00"
        },
        {
            "sequenceStoreId": "0123456789",
            "uploadId": "5290538638",
            "sourceFileType": "BAM",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "referenceArn": "arn:aws:omics:us-west-2:845448930428:referenceStore/8168613728/reference/2190697383",
            "name": "HG00146",
            "description": "BAM for HG00146",
            "creationTime": "2023-11-29T19:23:33.116516+00:00"
        },
        {
            "sequenceStoreId": "0123456789",
            "uploadId": "4174220862",
            "sourceFileType": "BAM",
            "subjectId": "mySubject",
            "sampleId": "mySample",
            "generatedFrom": "1000 Genomes",
            "referenceArn": "arn:aws:omics:us-west-2:845448930428:referenceStore/8168613728/reference/2190697383",
            "name": "HG00147",
            "description": "BAM for HG00147",
            "creationTime": "2023-11-29T19:23:47.007866+00:00"
        }
    ]
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的直接上傳至序列存放區。

若要取得讀取集啟用任務的清單

下列list-read-set-activation-jobs範例會取得 ID 為 之序列存放區的啟用任務清單1234567890。

aws omics list-read-set-activation-jobs \
    --sequence-store-id 1234567890

輸出：

{
    "activationJobs": [
        {
            "completionTime": "2022-12-06T22:33:42.828Z",
            "creationTime": "2022-12-06T22:32:45.213Z",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED"
        },
        {
            "creationTime": "2022-12-06T22:35:10.100Z",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "IN_PROGRESS"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要取得讀取集匯出任務的清單

下列list-read-set-export-jobs範例會取得 ID 為 之序列存放區的匯出任務清單1234567890。

aws omics list-read-set-export-jobs \
    --sequence-store-id 1234567890

輸出：

{
    "exportJobs": [
        {
            "completionTime": "2022-12-06T22:39:14.491Z",
            "creationTime": "2022-12-06T22:37:18.612Z",
            "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED"
        },
        {
            "creationTime": "2022-12-06T22:38:04.871Z",
            "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
            "id": "1234567890",
            "sequenceStoreId": "1234567890",
            "status": "IN_PROGRESS"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要取得讀取集匯入任務的清單

下列list-read-set-import-jobs範例會取得 ID 為 之序列存放區的匯入任務清單1234567890。

aws omics list-read-set-import-jobs \
    --sequence-store-id 1234567890

輸出：

{
    "importJobs": [
        {
            "completionTime": "2022-11-29T18:17:49.244Z",
            "creationTime": "2022-11-29T17:32:47.700Z",
            "id": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED"
        },
        {
            "completionTime": "2022-11-23T22:01:34.090Z",
            "creationTime": "2022-11-23T21:52:43.289Z",
            "id": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "sequenceStoreId": "1234567890",
            "status": "COMPLETED_WITH_FAILURES"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

列出序列存放區所請求分段上傳中的所有部分。

下列list-read-set-upload-parts範例會列出序列存放區所請求分段上傳中的所有部分。

aws omics list-read-set-upload-parts \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455 \
    --part-source SOURCE1

輸出：

{
    "parts": [
        {
            "partNumber": 1,
            "partSize": 94371840,
            "file": "SOURCE1",
            "checksum": "984979b9928ae8d8622286c4a9cd8e99d964a22d59ed0f5722e1733eb280e635",
            "lastUpdatedTime": "2023-02-02T20:14:47.533000+00:00"
        }
        {
            "partNumber": 2,
            "partSize": 10471840,
            "file": "SOURCE1",
            "checksum": "984979b9928ae8d8622286c4a9cd8e99d964a22d59ed0f5722e1733eb280e635",
            "lastUpdatedTime": "2023-02-02T20:14:47.533000+00:00"
        }
      ]

}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的直接上傳至序列存放區。

若要取得讀取集清單

下列list-read-sets範例會取得 ID 為 的序列存放區的讀取集清單1234567890。

aws omics list-read-sets \
    --sequence-store-id 1234567890

輸出：

{
    "readSets": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890/readSet/1234567890",
            "creationTime": "2022-11-23T21:55:00.515Z",
            "fileType": "FASTQ",
            "id": "1234567890",
            "name": "HG00146",
            "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "sampleId": "fastq-sample",
            "sequenceStoreId": "1234567890",
            "status": "ACTIVE",
            "subjectId": "fastq-subject"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要取得參考匯入任務的清單

下列list-reference-import-jobs範例會取得 ID 為 之參考存放區的參考匯入任務清單1234567890。

aws omics list-reference-import-jobs \
    --reference-store-id 1234567890

輸出：

{
    "importJobs": [
        {
            "completionTime": "2022-11-23T19:54:58.204Z",
            "creationTime": "2022-11-23T19:53:20.729Z",
            "id": "1234567890",
            "referenceStoreId": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "status": "COMPLETED"
        },
        {
            "creationTime": "2022-11-23T20:34:03.250Z",
            "id": "1234567890",
            "referenceStoreId": "1234567890",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "status": "IN_PROGRESS"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要取得參考存放區清單

下列list-reference-stores範例會取得參考存放區清單。

aws omics list-reference-stores

輸出：

{
    "referenceStores": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890",
            "creationTime": "2022-11-22T22:13:25.947Z",
            "id": "1234567890",
            "name": "my-ref-store"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要取得參考清單

下列list-references範例會取得 ID 為 之參考存放區的基因體參考清單1234567890。

aws omics list-references \
    --reference-store-id 1234567890

輸出：

{
    "references": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
            "creationTime": "2022-11-22T22:27:09.033Z",
            "id": "1234567890",
            "md5": "7ff134953dcca8c8997453bbb80b6b5e",
            "name": "assembly-38",
            "referenceStoreId": "1234567890",
            "status": "ACTIVE",
            "updateTime": "2022-11-22T22:27:09.033Z"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要取得執行群組的清單

下列list-run-groups範例會取得執行群組的清單。

aws omics list-run-groups

輸出：

{
    "items": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
            "creationTime": "2022-12-01T00:58:42.915219Z",
            "id": "1234567",
            "maxCpus": 20,
            "maxDuration": 600,
            "name": "cram-convert"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要取得任務清單

下列list-run-tasks範例會取得工作流程執行的任務清單。

aws omics list-run-tasks \
    --id 1234567

輸出：

{
    "items": [
        {
            "cpus": 1,
            "creationTime": "2022-11-30T23:13:00.718651Z",
            "memory": 15,
            "name": "CramToBamTask",
            "startTime": "2022-11-30T23:17:47.016Z",
            "status": "COMPLETED",
            "stopTime": "2022-11-30T23:18:21.503Z",
            "taskId": "1234567"
        },
        {
            "cpus": 1,
            "creationTime": "2022-11-30T23:18:32.315606Z",
            "memory": 4,
            "name": "ValidateSamFile",
            "startTime": "2022-11-30T23:23:40.165Z",
            "status": "COMPLETED",
            "stopTime": "2022-11-30T23:24:14.766Z",
            "taskId": "1234567"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要取得工作流程執行的清單

下列list-runs範例會取得工作流程執行的清單。

aws omics list-runs

輸出：

{
    "items": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
            "creationTime": "2022-12-02T23:20:01.202074Z",
            "id": "1234567",
            "name": "cram-to-bam",
            "priority": 1,
            "startTime": "2022-12-02T23:29:18.115Z",
            "status": "COMPLETED",
            "stopTime": "2022-12-02T23:57:54.428812Z",
            "storageCapacity": 10,
            "workflowId": "1234567"
        },
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
            "creationTime": "2022-12-03T00:16:57.180066Z",
            "id": "1234567",
            "name": "cram-to-bam",
            "priority": 1,
            "startTime": "2022-12-03T00:26:50.233Z",
            "status": "FAILED",
            "stopTime": "2022-12-03T00:37:21.451340Z",
            "storageCapacity": 10,
            "workflowId": "1234567"
        },
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
            "creationTime": "2022-12-05T17:57:08.444817Z",
            "id": "1234567",
            "name": "cram-to-bam",
            "status": "STARTING",
            "workflowId": "1234567"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要取得序列存放區清單

下列list-sequence-stores範例會取得序列存放區的清單。

aws omics list-sequence-stores

輸出：

{
    "sequenceStores": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:sequenceStore/1234567890",
            "creationTime": "2022-11-23T01:24:33.629Z",
            "id": "1234567890",
            "name": "my-seq-store"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

列出 a HealthOmics 分析資料的可用共用

下列list-shares範例會列出為資源擁有者建立的所有共用。

aws omics list-shares \
    --resource-owner SELF

輸出：

{
    "shares": [
        {
            "shareId": "595c1cbd-a008-4eca-a887-954d30c91c6e",
            "name": "myShare",
            "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/store_1",
            "principalSubscriber": "123456789012",
            "ownerId": "555555555555",
            "status": "PENDING"
        }
        {
            "shareId": "39b65d0d-4368-4a19-9814-b0e31d73c10a",
            "name": "myShare3456",
            "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/store_2",
            "principalSubscriber": "123456789012",
            "ownerId": "555555555555",
            "status": "ACTIVE"
        },
        {
            "shareId": "203152f5-eef9-459d-a4e0-a691668d44ef",
            "name": "myShare4",
            "resourceArn": "arn:aws:omics:us-west-2:555555555555:variantStore/store_3",
            "principalSubscriber": "123456789012",
            "ownerId": "555555555555",
            "status": "ACTIVE"
        }
    ]
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的跨帳戶共用。

若要取得標籤清單

下列list-tags-for-resource範例會取得 ID 為 之工作流程的標籤清單1234567。

aws omics list-tags-for-resource \
    --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567

輸出：

{
    "tags": {
        "department": "analytics"
    }
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的在 Amazon Omics 中標記資源。

若要取得變體匯入任務的清單

下列list-variant-import-jobs範例會取得變體匯入任務的清單。

aws omics list-variant-import-jobs

輸出：

{
    "variantImportJobs": [
        {
            "creationTime": "2022-11-23T22:47:02.514002Z",
            "destinationName": "my_var_store",
            "id": "69cb65d6-xmpl-4a4a-9025-4565794b684e",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "COMPLETED",
            "updateTime": "2022-11-23T22:49:17.976597Z"
        },
        {
            "creationTime": "2022-11-23T22:42:50.037812Z",
            "destinationName": "my_var_store",
            "id": "edd7b8ce-xmpl-47e2-bc99-258cac95a508",
            "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
            "runLeftNormalization": false,
            "status": "COMPLETED",
            "updateTime": "2022-11-23T22:45:26.009880Z"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

若要取得變體存放區清單

下列list-variant-stores範例會取得變體存放區清單。

aws omics list-variant-stores

輸出：

{
    "variantStores": [
        {
            "creationTime": "2022-11-23T22:09:07.534499Z",
            "id": "02dexmplcfdd",
            "name": "my_var_store",
            "reference": {
                "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
            },
            "status": "CREATING",
            "storeArn": "arn:aws:omics:us-west-2:123456789012:variantStore/my_var_store",
            "storeSizeBytes": 0,
            "updateTime": "2022-11-23T22:09:24.931711Z"
        },
        {
            "creationTime": "2022-09-23T23:00:09.140265Z",
            "id": "8777xmpl1a24",
            "name": "myvstore0",
            "status": "ACTIVE",
            "storeArn": "arn:aws:omics:us-west-2:123456789012:variantStore/myvstore0",
            "storeSizeBytes": 0,
            "updateTime": "2022-09-23T23:03:26.013220Z"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

若要取得工作流程清單

下列list-workflows範例會取得工作流程清單。

aws omics list-workflows

輸出：

{
    "items": [
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
            "creationTime": "2022-09-23T23:08:22.041227Z",
            "digest": "nSCNo/qMWFxmplXpUdokXJnwgneOaxyyc2YOxVxrJTE=",
            "id": "1234567",
            "name": "my-wkflow-0",
            "status": "ACTIVE",
            "type": "PRIVATE"
        },
        {
            "arn": "arn:aws:omics:us-west-2:123456789012:workflow/1234567",
            "creationTime": "2022-11-30T22:33:16.225368Z",
            "digest": "sha256:c54bxmpl742dcc26f7fa1f10e37550ddd8f251f418277c0a58e895b801ed28cf",
            "id": "1234567",
            "name": "cram-converter",
            "status": "ACTIVE",
            "type": "PRIVATE"
        }
    ]
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要匯入註釋

下列start-annotation-import-job範例會從 Amazon S3 匯入註釋。

aws omics start-annotation-import-job \
    --destination-name tsv_ann_store \
    --no-run-left-normalization \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --items source=s3://omics-artifacts-01d6xmpl4e72dd32/targetedregions.bed.gz

輸出：

{
    "jobId": "984162c7-xmpl-4d23-ab47-286f7950bfbf"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

若要啟用封存的讀取集

下列start-read-set-activation-job範例會啟用兩個讀取集。

aws omics start-read-set-activation-job \
    --sequence-store-id 1234567890 \
    --sources readSetId=1234567890 readSetId=1234567890

輸出：

{
    "creationTime": "2022-12-06T22:35:10.100Z",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "status": "SUBMITTED"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

匯出讀取集合

下列start-read-set-export-job範例會將兩個讀取集匯出至 Amazon S3。

   aws omics start-read-set-export-job \
       --sequence-store-id 1234567890 \
       --sources readSetId=1234567890 readSetId=1234567890 \
       --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ
\
       --destination s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/

輸出：

{
    "creationTime": "2022-12-06T22:37:18.612Z",
    "destination": "s3://omics-artifacts-01d6xmpl4e72dd32/read-set-export/",
    "id": "1234567890",
    "sequenceStoreId": "1234567890",
    "status": "SUBMITTED"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要匯入讀取集合

下列start-read-set-import-job範例會匯入讀取集。

aws omics start-read-set-import-job \
    --sequence-store-id 1234567890 \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --sources file://readset-sources.json

readset-sources.json 是具有下列內容的 JSON 文件。

[
    {
        "sourceFiles":
        {
            "source1": "s3://omics-artifacts-01d6xmpl4e72dd32/HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20101123.bam"
        },
        "sourceFileType": "BAM",
        "subjectId": "bam-subject",
        "sampleId": "bam-sample",
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890",
        "name": "HG00100"
    }
]

輸出：

{
    "creationTime": "2022-11-23T01:36:38.158Z",
    "id": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "sequenceStoreId": "1234567890",
    "status": "SUBMITTED"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要匯入參考基因體

下列start-reference-import-job範例會從 Amazon S3 匯入參考基因體。

aws omics start-reference-import-job \
    --reference-store-id 1234567890 \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --sources sourceFile=s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta,name=assembly-38

輸出：

{
    "creationTime": "2022-11-22T22:25:41.124Z",
    "id": "1234567890",
    "referenceStoreId": "1234567890",
    "roleArn": "arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ",
    "status": "SUBMITTED"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

執行工作流程

下列start-run範例會使用 ID 執行工作流程1234567。

aws omics start-run \
    --workflow-id 1234567 \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --name 'cram-to-bam' \
    --output-uri s3://omics-artifacts-01d6xmpl4e72dd32/workflow-output/ \
    --run-group-id 1234567 \
    --priority 1 \
    --storage-capacity 10 \
    --log-level ALL \
    --parameters file://workflow-inputs.json

workflow-inputs.json 是具有下列內容的 JSON 文件。

{
    "sample_name": "NA12878",
    "input_cram": "s3://omics-artifacts-01d6xmpl4e72dd32/NA12878.cram",
    "ref_dict": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict",
    "ref_fasta": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta",
    "ref_fasta_index": "omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.fasta.fai"
}

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:run/1234567",
    "id": "1234567",
    "status": "PENDING",
    "tags": {}
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

從 Amazon Omics 載入來源檔案

您也可以使用服務特定的 URIs，從 Amazon Omics 儲存體載入來源檔案。下列範例 workflow-inputs.json 檔案使用 Amazon Omics URIs 進行讀取集和參考基因體來源。

{
    "sample_name": "NA12878",
    "input_cram": "omics://123456789012.storage.us-west-2.amazonaws.com/1234567890/readSet/1234567890/source1",
    "ref_dict": "s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.dict",
    "ref_fasta": "omics://123456789012.storage.us-west-2.amazonaws.com/1234567890/reference/1234567890",
    "ref_fasta_index": "omics://123456789012.storage.us-west-2.amazonaws.com/1234567890/reference/1234567890/index"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要匯入變體檔案

下列start-variant-import-job範例會匯入 VCF 格式變體檔案。

aws omics start-variant-import-job \
    --destination-name my_var_store \
    --no-run-left-normalization  \
    --role-arn arn:aws:iam::123456789012:role/omics-service-role-serviceRole-W8O1XMPL7QZ \
    --items source=s3://omics-artifacts-01d6xmpl4e72dd32/Homo_sapiens_assembly38.known_indels.vcf.gz

輸出：

{
    "jobId": "edd7b8ce-xmpl-47e2-bc99-258cac95a508"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

標記資源

下列tag-resource範例會將department標籤新增至 ID 為 的工作流程1234567。

aws omics tag-resource \
    --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567 \
    --tags department=analytics

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的在 Amazon Omics 中標記資源。

從資源中移除標籤

下列untag-resource範例會從工作流程中移除department標籤。

aws omics untag-resource \
    --resource-arn arn:aws:omics:us-west-2:123456789012:workflow/1234567 \
    --tag-keys department

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

若要更新註釋存放區

下列update-annotation-store範例會更新名為 的註釋存放區描述my_vcf_store。

aws omics update-annotation-store \
    --name my_vcf_store \
    --description "VCF annotation store"

輸出：

{
    "creationTime": "2022-12-05T18:00:56.101860Z",
    "description": "VCF annotation store",
    "id": "bd6axmpl2444",
    "name": "my_vcf_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "ACTIVE",
    "storeFormat": "VCF",
    "updateTime": "2022-12-05T18:13:16.100051Z"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

更新執行群組

下列update-run-group範例會更新 ID 為 的執行群組設定1234567。

aws omics update-run-group \
    --id 1234567 \
    --max-cpus 10

輸出：

{
    "arn": "arn:aws:omics:us-west-2:123456789012:runGroup/1234567",
    "creationTime": "2022-12-01T00:58:42.915219Z",
    "id": "1234567",
    "maxCpus": 10,
    "maxDuration": 600,
    "name": "cram-convert",
    "tags": {}
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics 工作流程。

若要更新變體存放區

下列update-variant-store範例會更新名為 的變體存放區描述my_var_store。

aws omics update-variant-store \
    --name my_var_store \
    --description "variant store"

輸出：

{
    "creationTime": "2022-11-23T22:09:07.534499Z",
    "description": "variant store",
    "id": "02dexmplcfdd",
    "name": "my_var_store",
    "reference": {
        "referenceArn": "arn:aws:omics:us-west-2:123456789012:referenceStore/1234567890/reference/1234567890"
    },
    "status": "ACTIVE",
    "updateTime": "2022-12-05T18:23:37.686402Z"
}

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Analytics。

更新工作流程

下列update-workflow範例會更新 ID 為 的工作流程描述1234567。

aws omics update-workflow \
    --id 1234567 \
    --description "copy workflow"

如需詳細資訊，請參閱 Amazon Omics 開發人員指南中的 Omics Storage。

上傳讀取集合部分。

下列upload-read-set-part範例會上傳讀取集的指定部分。

aws omics upload-read-set-part \
    --sequence-store-id 0123456789 \
    --upload-id 1122334455 \
    --part-source SOURCE1 \
    --part-number 1 \
    --payload /path/to/file/read_1_part_1.fastq.gz

輸出：

{
    "checksum": "984979b9928ae8d8622286c4a9cd8e99d964a22d59ed0f5722e1733eb280e635"
}

如需詳細資訊，請參閱 AWS HealthOmics 使用者指南中的直接上傳至序列存放區。