Instructions on how to restart run upload to BaseSpace using BaseSpace Broker

The following instructions can be used when a run is stuck in uploading status in BaseSpace Sequence Hub (BSSH).

This method of restarting the run upload can only be used for the following Illumina sequencers and corresponding software versions which have BaseSpace Broker installed.

• HiSeq X/3000/4000

• HiSeq 2500

• NextSeq 500/550 with NextSeq Control Software (NCS) v1 and v2

• MiSeq

• MiniSeq

Table 1. Service used to upload run files to BaseSpace (BSSH)

Instrument	Service used to transfer files to BaseSpace	Service used to transfer files to server/output
NovaSeq 6000	Universal Copy Service (UCS)	Universal Copy Service (UCS)
HiSeq X/3K/4K	BaseSpace Broker	Run Copy Service
HiSeq 2500	BaseSpace Broker	RTA 1
NextSeq 500/550 (NCS v1 & v2)	BaseSpace Broker	Run Copy Service
NextSeq 500/550 (NCS v3 & v4)	Universal Copy Service (UCS)	Universal Copy Service (UCS)
MiSeq (MCS v2 & v3)	BaseSpace Broker	RTA 1
MiSeq (MCS v4)	Universal Copy Service (UCS)	Universal Copy Service (UCS)
MiniSeq (MnCS v2)	BaseSpace Broker	Run Copy Service
MiniSeq (MnCS v3)	Universal Copy Service (UCS)	Universal Copy Service (UCS)
iSeq 100	Universal Copy Service (UCS)	Universal Copy Service (UCS)
NextSeq 1000/2000	Universal Copy Service (UCS)	Universal Copy Service (UCS)

The BaseSpace Broker functions as a Service on the instrument, running as a background process.​

Once a run starts uploading, two files will be created in D/Illumina/BaseSpaceBroker:​

​1. BrokerSate.BaseSpaceServiceConnection_[RUNID].xml​

• Contains a list of files to be uploaded.​

1. BrokerSate.BaseSpaceServiceConnection_[RUNID].dat ​

• Contains a list of files that have uploaded.​

​As the upload progresses, the file size of the .xml decreases and the file size of the .dat increases;​ ​this shows if file transfer is actively occurring.

To Restart BaseSpace Broker:

1. First, make sure that the instrument date and time match the local time zone where the instrument is located.

2. Navigate to the Task Manager (right click on the task bar or CTRL + ALT + DEL).

3. Navigate to the services tab, locate Illumina BaseSpace Broker, right click on it, and select "Stop Service." If the service is already stopped, continue to the steps below.

4. Once the broker is Stopped, navigate to directory D:\Illumina\BaseSpaceBroker.

5. In this directory, there should only be one .dat and one .xml file representing the most recent run. If there is only one .xml file, continue to the steps below. If there are more than two files, move any files that do not have the most recent BaseSpace Run ID to the Archive folder.

6. Navigate to the Task Manager > Services > BaseSpace Broker, then right click and select "Start Service."

7. Once the service is restarted, the .dat will increase in size, the upload will continue, and eventually, the run status will show as 'Pending analysis' in BaseSpace.

For any feedback or questions regarding this article (Illumina Knowledge Article #1811), contact Illumina Technical Support [e-mail].