Applied Biosystems SOLiD Software v3.0.

2 Release Notes
© Copyright 2009 Applied Biosystems. All Rights Reserved.
May 2009

TABLE OF CONTENTS
1. OVERVIEW
2. ISSUES FIXED in v3.0.2
3. ISSUES FIXED in v3.0.1
4. SOLiD™ System Software INSTALLATION
5. GlobalSETS INSTALLATION
6. KNOWN ISSUES
7. LEGAL STATEMENTS

1. OVERVIEW
Applied Biosystems provides SOLiD™ Software Suite for SOLiD™ 3 Analyzer. Each software
component and tool in the SOLiD™ Software Suite provides easy-to-use steps for an end user for operating
the instrument, automatic data analysis to integrating tertiary data analysis packages.
(http://www.appliedbiosystems.com/solidsoftware)
• SOLiD™ Instrument Control Software (ICS)
• SOLiD ™ Experiment Tracking Systems (SETS)
• SOLiD™ Analysis Tools (SAT)
• SOLiD™ Applications Interface (SAI)

SOLiD™ Software Suite v3.0.2 is a maintenance release.

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2. ISSUES FIXED in v3.0.2

2.1. Instrument Control Software (ICS)

• ICS - URL for displaying SETS via ICS link is incorrect for WFA reports.

2.2. Data Analysis

Secondary analysis
• In some cases there were inconsistent results in matching results.
• Matching stats mega coverage reports incorrect results for big ma data.

3. ISSUES FIXED in v3.0.1

3.1. Instrument Control Software (ICS)

• If the user ran the load/clear scripts with the door open, the Robot "emergency stop" error
message would intermittently pop up.
• Primary or Secondary Analysis failed to execute in the following situation: If the Primary
Analysis or Secondary Analysis settings were highlighted and the user selects the “Back”
button followed by the “Next” button in the Create Run Wizard, the previously highlighted
analysis setting was missing. This resulted in the failure to generate the appropriate data.

• When pausing a run while performing the Image operation of a Focal Map or Cycle Scan, the
error message Imaging System Error was generated. The system would pause for the Flow
Cell that was performing the imaging operation. The other Flow Cell was not affected.

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 • ‘Shutdown Linux’ in the shutdown wizard could fail because of the mismatch of the user
name and password
• Stage registration was compromised particularly for high density beads.
• Out of focus images were found in some cases due to the low image quality threshold.
• User could only pause at certain stages. In v3.0.2, the user can pause at any time during
fluidic modules, as long as the user selects 'Pause after this module has been completed'
when pausing and 'resume' when resuming.
• When a barcode cycle was repeated after BC completes and the second workflow has a "non-
barcode", barcode job displayed as "barcodeNull" in SETS.
• DMCB power down and power up (this should never happen after the instrument is setup)
might lead to alignment issue.
• The full slide mask had some "typewriter" behavior at both the bottom and top of the slide.
It scanned from left to right, and then reset to the left instead of scanning back to the left.
These long moves, especially during rescues, could cause some oblong images.
• Lamp shut down button may shorten the lamp lifespan. In v3.0.2, the button “Lamp On/Off”
is removed.
• Long run names cause image browser to generate an exception

3.2. SOLiD™ Experiment Tracking System (SETS)

• "Edit Pipelines" page did not handle dependencies properly.

• 404 error occurred for WFA reports
• # beads/# matching beads in the Matching Summary Report was wrong for a mate pair library
analysis

3.3. Data Analysis

Primary Analysis
• A minor error was found in the method for subpixel image shifting that appeared to decrease
run yield by a few percent.
Secondary analysis
• Out of memory error for a large run occurred at the SingleTag pipeline
• Progressive mapping throughput was missing in Matching Stats file
• Mapping performance was suboptimal due to Mapreads Schema inefficiency
• For progressive mapping for both MatchRepeat and MatchRandom pipeline, setting parameter
“Remove Matched Reads” (in SETS) to ‘false’ has limited usage. Therefore, the parameter is
removed from SETS in v3.0.2 and “Remove Matched Reads” is “True” by default.
• Incorrect reference length in matching stats files for a reference containing more than one
sequences.

3.4. Compute System (Linux Configuration)

• Filesystem locking could fail on /data/results nfs mounts on compute nodes,

• There were too many open files errors for IQ runs
• Nameservers associated with AB in /etc/resolv.conf caused delay in DNS name resolution

3.5. Issues derived from SOLiD™ v3.0 Installers

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 • In rpm upgrade: primary analysis folder was added to a wrong location and caused secondary
analysis and BC run to fail
• Folder structure of runs with libraries was corrupted after 3.0 upgrade
• Cleanup script deleted null_secondary_settings

4. SOLiD™ System Software v3.0.2 Installation

Download the installers from Applied Biosystems web site.
http://www.appliedbiosystems.com/support/software/
There are four installers in the zipped file. The installers will upgrade both v3.0 & v3.0.1 to
v3.0.2.
• ICS v3.0.2 executable for Windows XP
• Image Browser executable for Windows XP
• SETS-SAT v3.0.2 executable for Windows XP
• SETS-SAT v3.0.2 tar file (use it for GlobalSETS upgrade) for Linux command line install

For upgrading software on the instrument, install all of the following components.
• ICS v3.0.2 executable for Windows XP
• Image Browser executable for Windows XP
• SETS-SAT v3.0.2 executable for Windows XP

For upgrading GlobalSets on an offline compute cluster, install following

components
• SETS-SAT v3.0.2 tar file (use it for GlobalSETS upgrade) for Linux command line install

4.1. Before Installation

• **Make sure that the media used to download the installers is VIRUS-FREE. The media
should be scanned by an Anti-Virus software before being put on the instrument
computer, or reformatted before downloading updaters.
• Make sure that the instrument and the computer are not being used. SETS-SAT
installer would exit if any analysis is running. It will only install if the compute cluster is
idle.

To check whether an analysis is running or not:

• Launch SETS
• Click on VIEW tab,
• Select ‘Cluster Status’
• Look for queue statistics section for any jobs
It is idle, if all the values are 0.
Following is an example of the cluster status from SETS.

Current analysis jobs

Job Date
Job Id Progress Analysis 3ame Run 3ame Sample 3ame
3ame Started
Queue statistics
0 of 3 Nodes Active (0.00%)
Total Jobs: 0
Active Jobs: 0
Idle Jobs: 0
Blocked
0
Jobs:

Queue # of running jobs # of queued jobs

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 Queue # of running jobs # of queued jobs
pipeline 0 0
reanalyze 0 0

tracking 0 0

secondary 0 0

batch 0 0

feedback 0 0

interactive 0 0

4.2. Instrument Control Software (ICS) v3.0.2 Installation

Perform upgrade after all the runs are complete and cleared from
the flowcells. Shutdown the ICS application. Do not un-install
v3.0 or v3.0.1 ICS software. Double click on the patch installer,
setup.exe, and follow the installation instruction. After
successful installation, v3.0.2 should be displayed on the
application title bar and the about box.

4.3. Image Browser v3.0.2

Uninstall the previously installed Image Browser by selecting
Control Panel -> Add or Remove Programs. Click on the Remove
button. Follow the steps to uninstall Image Browser.

Double click on the setup.exe from the Image Browser installer.

Follow the installation instruction. After successful
installation, the about box displays version 3.0.2.

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4.4. SETS & SATS v3.0.2 Installation through Windows XP

1. Double click “SETS-SAT v3.0.2.exe” and follow the instruction on

the screen

2. Accept the License agreement in the following screen

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3. After accepting the license agreement, you will see the following screen which shows the
progress of installation. This window will close on its own once the installation is
complete.

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4. After the installation is complete you will see the following text file which shows the log
messages from rpm install. You can make a copy of this log messages by clicking on
File->Save As.

5. Click “Finish” to exit the installer

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 6. Go to sets page and click Help->About. It shows version as
3.0r25.2-31661M

4.5. After Installation

If there are custom plugins implemented in v3.0 & v3.0.1, copy the Plugins from previous
directory (/share/apps/corona-old-version) to the new directory.

5. SOLiD™ Global SETS Software v3.0.2 installation

Download the SETS-SATv3.0.2.tar installer onto the headnode.

Follow following steps to perform this update to GlobalSETS on a standalone compute Cluster
(offline cluster)

1) Download SETS-SATv3.0.2.tar file to /opt directory as root

2) Unzip using the following command
a. tar –xvf SETS-SATv3.0.2.tar
3) Change to SETS-SATv3.0.2 to directory and run install.sh script
a. cd SETS-SATv3.0.2/
b. ./install.sh
c. Press y when prompted.

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 4) If there are custom plugins implemented in v3.0 & v3.0.1, copy the Plugins from previous
directory (/share/apps/corona-old-version) to the new directory.

6. KNOWN ISSUES

.
• Auto focus range detection didn’t work 100% of the time. If auto-detection is used, please
verify by taking and checking the images of the beads. If auto-detection is not able to focus on
the beads, please resort back to manual focusing as in v2.
• If you repeat a barcode cycle after barcode job has already completed for the F3 tag, the data
will not be re-partitioned using the new barcode data. The barcode job partitions and saves
the results of primary analysis for the F3 tag to the libraries/<library name> folders, then
removes the redundant overall primary results originally generated by Filter Fasta. If a
barcode cycle is repeated, the overall results for F3 are no longer available. Workaround: re-
analyze primary in SETS. This will repeat Filter Fasta for F3, thus regenerating the needed
input for the subsequent barcode job to correctly partition the data.

• As a side effect of correcting the type writer behavior of the full slide mask in v3.0, the old
slide is renamed to ".1_spot_mask_sf". After upgrading to v3.0.2, if there are pending runs in
"Manage Runs" view that are still referring to the old mask ".1_spot_mask_sf", the runs need
to be re-created after the old runs are deleted from SETS to prevent run name collision.

7. LEGAL STATEMENTS

For Research Use Only. Not for use in diagnostic procedures.

Notice to Purchaser: License Disclaimer

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Purchase of this software product alone does not imply any
license under any process, instrument or other apparatus, system,
composition, reagent or kit rights under patent claims owned or
otherwise controlled by Life Technologies, either expressly, or
by estoppel.

Applied Biosystems, and AB (Design) are registered trademarks of

Life Technologies or its subsidiaries in the US and/or certain
other countries.
All other trademarks are the sole property of their respective
owners.

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