AWS CLI Command Reference

Note:

You are viewing the documentation for an older major version of the AWS CLI (version 1). To view this page for the AWS CLI version 2, click here.

We announced the upcoming end-of-support for the AWS CLI v1. For dates, additional details, and information on how to migrate, please refer to the linked announcement. For more information see the AWS CLI version 2 installation instructions and migration guide.

[ aws . omics ]

get-read-set-metadata

Description

Retrieves the metadata for a read set from a sequence store in JSON format. This operation does not return tags. To retrieve the list of tags for a read set, use the ListTagsForResource API operation.

See also: AWS API Documentation

Synopsis

  get-read-set-metadata
--id <value>
--sequence-store-id <value>
[--cli-input-json <value>]
[--generate-cli-skeleton <value>]
[--debug]
[--endpoint-url <value>]
[--no-verify-ssl]
[--no-paginate]
[--output <value>]
[--query <value>]
[--profile <value>]
[--region <value>]
[--version <value>]
[--color <value>]
[--no-sign-request]
[--ca-bundle <value>]
[--cli-read-timeout <value>]
[--cli-connect-timeout <value>]
[--v2-debug]

Options

--id (string)

The read set’s ID.

--sequence-store-id (string)

The read set’s sequence store ID.

--cli-input-json (string) Performs service operation based on the JSON string provided. The JSON string follows the format provided by --generate-cli-skeleton. If other arguments are provided on the command line, the CLI values will override the JSON-provided values. It is not possible to pass arbitrary binary values using a JSON-provided value as the string will be taken literally.

--generate-cli-skeleton (string) Prints a JSON skeleton to standard output without sending an API request. If provided with no value or the value input, prints a sample input JSON that can be used as an argument for --cli-input-json. If provided with the value output, it validates the command inputs and returns a sample output JSON for that command.

Global Options

--debug (boolean)

Turn on debug logging.

--endpoint-url (string)

Override command’s default URL with the given URL.

--no-verify-ssl (boolean)

By default, the AWS CLI uses SSL when communicating with AWS services. For each SSL connection, the AWS CLI will verify SSL certificates. This option overrides the default behavior of verifying SSL certificates.

--no-paginate (boolean)

Disable automatic pagination. If automatic pagination is disabled, the AWS CLI will only make one call, for the first page of results.

--output (string)

The formatting style for command output.

  • json
  • text
  • table

--query (string)

A JMESPath query to use in filtering the response data.

--profile (string)

Use a specific profile from your credential file.

--region (string)

The region to use. Overrides config/env settings.

--version (string)

Display the version of this tool.

--color (string)

Turn on/off color output.

  • on
  • off
  • auto

--no-sign-request (boolean)

Do not sign requests. Credentials will not be loaded if this argument is provided.

--ca-bundle (string)

The CA certificate bundle to use when verifying SSL certificates. Overrides config/env settings.

--cli-read-timeout (int)

The maximum socket read time in seconds. If the value is set to 0, the socket read will be blocking and not timeout. The default value is 60 seconds.

--cli-connect-timeout (int)

The maximum socket connect time in seconds. If the value is set to 0, the socket connect will be blocking and not timeout. The default value is 60 seconds.

--v2-debug (boolean)

Enable AWS CLI v2 migration assistance. Prints warnings if the command would face a breaking change after swapping AWS CLI v1 for AWS CLI v2 in the current environment. Prints one warning for each breaking change detected.

Examples

Note

To use the following examples, you must have the AWS CLI installed and configured. See the Getting started guide in the AWS CLI User Guide for more information.

Unless otherwise stated, all examples have unix-like quotation rules. These examples will need to be adapted to your terminal’s quoting rules. See Using quotation marks with strings in the AWS CLI User Guide .

To view a read set

The following get-read-set-metadata example gets details about a read set’s files.

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

Output:

{
    "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"
}

For more information, see Omics Storage in the Amazon Omics Developer Guide.

Output

id -> (string)

The read set’s ID.

arn -> (string)

The read set’s ARN.

sequenceStoreId -> (string)

The read set’s sequence store ID.

subjectId -> (string)

The read set’s subject ID.

sampleId -> (string)

The read set’s sample ID.

status -> (string)

The read set’s status.

name -> (string)

The read set’s name.

description -> (string)

The read set’s description.

fileType -> (string)

The read set’s file type.

creationTime -> (timestamp)

When the read set was created.

sequenceInformation -> (structure)

The read set’s sequence information.

totalReadCount -> (long)

The sequence’s total read count.

totalBaseCount -> (long)

The sequence’s total base count.

generatedFrom -> (string)

Where the sequence originated.

alignment -> (string)

The sequence’s alignment setting.

referenceArn -> (string)

The read set’s genome reference ARN.

files -> (structure)

The read set’s files.

source1 -> (structure)

The location of the first file in Amazon S3.

totalParts -> (integer)

The file’s total parts.

partSize -> (long)

The file’s part size.

contentLength -> (long)

The file’s content length.

s3Access -> (structure)

The S3 URI metadata of a sequence store.

s3Uri -> (string)

The S3 URI for each read set file.

source2 -> (structure)

The location of the second file in Amazon S3.

totalParts -> (integer)

The file’s total parts.

partSize -> (long)

The file’s part size.

contentLength -> (long)

The file’s content length.

s3Access -> (structure)

The S3 URI metadata of a sequence store.

s3Uri -> (string)

The S3 URI for each read set file.

index -> (structure)

The files’ index.

totalParts -> (integer)

The file’s total parts.

partSize -> (long)

The file’s part size.

contentLength -> (long)

The file’s content length.

s3Access -> (structure)

The S3 URI metadata of a sequence store.

s3Uri -> (string)

The S3 URI for each read set file.

statusMessage -> (string)

The status message for a read set. It provides more detail as to why the read set has a status.

creationType -> (string)

The creation type of the read set.

etag -> (structure)

The entity tag (ETag) is a hash of the object meant to represent its semantic content.

algorithm -> (string)

The algorithm used to calculate the read set’s ETag(s).

source1 -> (string)

The ETag hash calculated on Source1 of the read set.

source2 -> (string)

The ETag hash calculated on Source2 of the read set.

creationJobId -> (string)

The read set’s creation job ID.