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A blinking red light on the instrument may indicate that a hardware component has failed or a possible communication disruption has occurred between the instrument and computer. Completely shut down the instrument, wait for 2 minutes, and then start up in the order documented in Applied Biosystems™ 3730/3730xl DNA Analyzers: Starting Up the Instrument Technical Note or the Applied Biosystems™ 3730/3730xl DNA Analyzer Getting Started Guide.

If the instrument goes from a flashing amber light to red light, one or more of the hardware components has failed the hardware diagnostic and a service call should be opened up. 

The amber light starts to blink once the instrument has logged onto the computer using the <instrument name>User account (e.g. 3730User). Anything that prevents it from connecting will cause the amber light to remain solid. Some of the more frequent reasons for this happening include:

  • User password has expired or changed
  • Firewall is on
  • Cable is plugged into the wrong port
  • The wrong network card was configured to connect to the local network
  • Bad network card

A perpetually blinking amber light usually indicates that there is a door open on the instrument or a bad door sensor. Open the main door, the oven door and the detector cell door (small black door with the laser warning on it) and close them again. After the autosampler stops moving the light should change to green. If the amber light does not go to green, it is possible that a door sensor is not working properly and a service call may be required. 

Some of the other causes of an Unstable Electrophoresis current detected error message are:

  • Leak on the system
  • Polymer that:
    • Has expired
    • Has been left on the instrument for more than the recommended time
    • Is a mixture of expired polymer and non-expired polymer
  • Using Running Buffer that was:
    • Diluted to 1X incorrectly
    • Swapped with the water position on the Autosampler deck
    • On the instrument longer than 48 hours 
    • Not filled to the fill line or evaporated below the fill line 
  • An arcing event that was not cleaned afterwards using the water wash wizard
  • Not performing regular maintenance on the instrument
  • Hardware issues

Inspect the system for leaks. If you do not see any leaks on the system, perform a water wash using the water wash wizard and place fresh, non-expired polymer and freshly made 1X Running Buffer on the system. If the problem persists, a service call may be required.

“Leak detected” error messages can also occur when the piston on the pump moves further than expected during the movement of the pump. The usual cause for this is a leak on the system, usually due to either an improperly tightened or improperly threaded fitting or a broken capillary. However, if this is not observed, some of the other reasons are:

  • Valve stuck in open position
  • Large air bubble under the piston
  • Polymer:
    • Wrong polymer type (e.g., instrument thinks it has POP™-7 on it but it really has POP™-4).
    • Old/degraded polymer 
  • Improper/no maintenance on the system

Inspect the system for leaks. If you do not see any leaks on the system, perform a water wash using the water wash wizard and place fresh, non-expired polymer and freshly made 1X Running Buffer on the system. If the problem persists, a service call may be required.

The location of the files is determined by the Results Group. Double check the Location tab in the Results Group selected for the run to make sure it has not been changed and the files saved to a different location. 

On the Applied Biosystems™ 3730/3730xl DNA Analyzer, you can click on Run History in the Data Collection Software, select your plate and go to the Re-extraction heading under Run History to try and recover the data files. 

Some other causes of missing data include:

  • If the system is networked and something interrupts the network connection then it might interrupt the connection between the instrument and the computer. Depending on when it occurred, you might be able to recover it on Re-extraction. If you are saving the samples to a network drive and the location is unavailable, the data may still be in the Oracle Database on the Applied Biosystems™ 3130/3130xl Genetic Analyzer and can be re-extracted. 
  • If the septa is old/re-used. We officially recommend that the plate septa be used one time only. However, we are aware that some of our customers will rinse the septa with water and re-use them. In those instances, the septa can become sticky and gummy over time and eventually start sticking to the array. In the best case scenario, the array will lift the plate off of the autosampler just enough to break the connection with the plate sensor and abort the run. The Event Log might show that the run aborted due to the user aborting it, so the run will appear to have completed or stopped with no errors and no data. Worst case scenario is that the plate remains on array as the autosampler starts to move, bending the electrodes and breaking the array. Replace the plate septa regularly (each run is recommended, but after no more than 4–5 rinses; no not use bleach, detergents, or solvents to clean the septa, it will cause them to dry out faster and risks contaminating the system). 
  • Completely shut down the instrument and computer. Wait 2 minutes and restart the computer, log in, then turn on the instrument and wait for the green light. 
  • Right click on “Computer” and select “Manage”. Expand “Services and Applications” and click on “Services”
  • Scroll down to “Oracle” in the list on the right. Any Oracle service that has a startup type of “Automatic” should have a Status of “Started”. If not, select the service and click Start. After the services have started, wait 2 minutes and then try to launch the Data Collection Software. 

If the services do not start or if this does not resolve the issue, please contact Technical Support at techsupport@thermofisher.com for further assistance. This symptom may require a service call.

If the system has not been started in the last week, completely shut off the instrument and the computer, wait for 2 minutes and restart it in the order in the Applied Biosystems™ 3730/3730xl DNA Analyzers: Starting Up the Instrument Technical Note or the Applied Biosystems™ 3730/3730xl DNA Analyzer Getting Started Guide.

If the computer itself seems to be running slowly after restarting, you may need to defragment the hard drives. For the Applied Biosystems™ 3730/3730xl DNA Analyzer, only defragment the C and E drives. Do not defragment the D and F drives—the Oracle database is installed on these drives and defragmenting the Oracle drive may cause functionality issues with your Data Collection and GeneMapper™ software. 

If the system has been restarted and the computer slowdown is limited to the instrument Data Collection Software, it’s possible that the database/data store is getting full. For the Applied Biosystems™ 3730/3730xl DNA Analyzer, after the Data Collection software has launched select “Database Manager” on the left side. If there are more than 300 runs or the database is greater than 10% full, you will need to click the Cleanup button to remove all Processed plates in order to increase the speed of the system. Should the database remain this way or continue to get filled, it will eventually hit a point where it will lock up and a service call will need to be opened for re-imaging and re-installation. 

It is not unusual to see a large bubble at the tip of the piston while performing the water wash wizard on the system. When the polymer is put back on to the system, the difference in viscosity is usually enough to dislodge the bubble and push it out. In extreme cases, it may be necessary to repeat the wash and go back and forth between the water and polymer to force it out. 

It is possible that the polymer tube fitting may not be screwed into the pump properly, allowing air to get pulled in as the piston retracts. It is also possible that some debris may be stuck in the check valve, locking it in the open position. It may be necessary to detach and carefully attach the polymer tube again and then perform a water wash wizard to remove the bubbles and clear any debris from the check valve. 

If the array is stuck in the pump, even after loosening the knob, squirt around the edge of the array head with distilled water and try to remove it again. If the array will not move, a service call may be required. Do not use excessive force or tools to try and remove it. 

When placing the array on the instrument, the last step in the process is to loosen the array knob and the instrument forces any air bubbles around the array tip through the threading and the middle of the array knob. Some polymer gets pushed through as well and when it dries up, it appears as a white, flaky residue. Use a damp, lint-free cloth to remove it. If more residue appears after the cleanup, it is possible that the array knob is not tightened enough or the array ferrule may require replacement. 

It is possible that the instrument and computer had a communication issue, disassociating the data from the plate record, resulting in no history and no data files. If this happens, shut down the instrument and the computer, wait 2 minutes and restart the system following the instructions in the Applied Biosystems™ 3730/3730xl DNA Analyzers: Shutting Down the Instrument and Applied Biosystems™ 3730/3730xl DNA Analyzers: Starting Up the Instrument Technical Notes.

Installation of the Data Collection Software for the Applied Biosystems™ 3730/3730xl DNA Analyzer is a complex process that requires a Field Service Engineer to install the software properly. 

You can purchase a computer for installation of the secondary analysis software packages (e.g., Sequencing Analysis, GeneMapper™ software) as long as the computer meets the software compute requirements (for processor speed, the minimum speed of the processor should be at least 3 GHz) and you can install the software yourself. 

For the instrument computer, the computer system has a much more stringent requirement and undergoes thorough testing to make sure it can handle the flow of data from the instrument to the computer. The images for the computer system are streamlined to make sure they have the proper drivers for the computer components and the Operating System optimized to make sure there is nothing running in the background that might slow the computer down, take up memory, or conflict with our software. Purchasing a computer commercially can introduce too many variables in terms of hardware and software that can negatively affect the data collection process so we cannot support connecting it to the instrument.