10 Troubleshooting

Sources of Problems, 10-2

System Problems, 10-2
Error Messages, 10-3
Problems in Power-Up, 10-8
Problems with System Performance, 10-9
Problems with an Alpha Unit, 10-10
Problems Related to Protocols, 10-10
Problems due to Environmental Conditions, Setup, and Maintenance, 10-13
 DNA Engine Dyad Operations Manual

Sources of Problems
The Dyad cycler is designed to handle even the most stringent thermal-cycling requirements.
A major strength of the Dyad cycler is its flexibility, which allows multifaceted and demand-
ing cycling protocols to be implemented with the greatest of experimental and programming
ease. However, occasional problems may still be encountered.

Problems can result in a number of ways. We group them as follows:

• System problems
• Problems in power up
• Problems in system performance
• Problems with Alpha units
• Problems due to environmental conditions, setup, and maintenance
• Problems related to protocols
When troubleshooting a difficulty, it is advisable to have the following pieces of information
available, should it become necessary to contact MJ Research, Inc. for assistance:

• Serial and catalog numbers for the base as well as Alpha units
• Exact nature of the problem
• Frequency of the problem (i.e., is the problem repeatable)
• Steps already taken to troubleshoot the problem (i.e., controls performed)

System Problems
The Status window was reviewed in Chapters 5, 6, and 7, covering the creation, editing,
and running of programs. For a review of the basic menus of this window, please review
these chapters.

In the Status window, the <View> submenu allows the user to view the <Error Log>. Entries
will be made to this log if a user terminates a program before its end, if the cycler terminates
a program before end, or if the cycler encounters a serviceable issue before the termination
of the program, but was able to complete the program. Problems and error messages can
either be cycler or Alpha unit specific. In each case, a recommended action is listed and
should be followed. Under no circumstances should a customer attempt service of a Dyad
cycler or an Alpha unit, as this will result in a voided warranty and may not result in complete
problem resolution. The only exception would be minor maintenance of the units, such as,
removal of vent blockage or routine cleaning, as outlined in Chapter 9.

10-2
 Troubleshooting

Table 10-1: Error Messages

The Error Codes listed in the table below correspond to the error codes returned in the Dyad
cycler’s <Error Log>. The Remote Error Codes listed correspond to the error codes returned
when the Dyad cycler is operated in remote mode (see the <Remote> and <Auto Remote>
sections in Chapter 8 for more information on remote mode).

Note: The Dyad system software is quite sensitive to block and heat-sink errors for these can
affect accuracy and performance. When such error messages occur, try restarting the proto-
col. If the message fails to reappear, proceed as usual.

Remote Error Code Reason Action

Error Code
Call (888) MJ CYCLE (in the US
This sample block reached a
or Canada), or your local
1 BO higher temperature than was
distributor (outside the US or
expected.
Canada).
An irregularity was detected in
the block's center temperature
sensor. The sensor will be
16 BSF-CI checked automatically during No action required at this time.
and after the run, and you will
be notified if any persistent
problem is found.
An irregularity was detected in
the block's left temperature
sensor. The sensor will be
19 BSF-LI checked automatically during No action required at this time.
and after the run, and you will
be notified if any persistent
problem is found.
An irregularity was detected in
the sensitivity of the block's right
temperature sensor. The sensor
17 BSF-RI will be checked automatically No action required at this time.
during and after the run, and
you will be notified if any
persistent problem is found.
An irregularity was detected in
one or more of the block's
temperature sensors. The Call (888) MJ CYCLE (in the US
4 BSF-PT sensor was checked and the or Canada), or your local
results show an inaccuracy in distributor (outside the US or
block temperature measurement. Canada).
Your program was
automatically stopped.
The heated lid is not pre- Recover samples and call (888)
heating correctly. Your samples MJ CYCLE (in the US or
6 HLF have remained at room Canada), or your local distributor
temperature, and your program (outside the US or Canada).
was never started.

10-3
 DNA Engine Dyad Operations Manual

Remote
Error Code Reason Action
Error Code
Please observe the following
guidelines: 1) place instruments
at least 10cm apart, 2) avoid
placing instruments in any
location where hot air might
The heat sink temperature is enter the intake vents, 3) place
registering somewhat higher instrument on a hard surface with
than normal. Power levels will no debris or paper underneath,
be scaled back slightly until the 4) clean all air vents and Alpha
8 HSO
heat sink temperatue returns to unit fins of dust and debris, 5)
normal. Adequate airflow is avoid running the instrument in
necessary to prevent the heat areas with ambient temperatures
sink from overheating. above 25°C. Continue to use the
instrument. If problem reoccurs
please call (888) MJ CYCLE (in
the US or Canada), or your local
distributor (outside the US or
Canada).

Please observe the following

guidelines: 1) place instruments
at least 10cm apart, 2) avoid
placing instruments in any
location where hot air might
The heat sink reached a enter the intake vents, 3) place
temperature higher than instrument on a hard surface with
normal, and the program was no debris or paper underneath,
2 HSO-PT automatically stopped. 4) clean all air vents and Alpha
Adequate airflow is necessary to unit fins of dust and debris, 5)
prevent the heat sink from avoid running the instrument in
overheating. areas with ambient temperatures
above 25°C. If the problem
reoccurs please call (888) MJ
CYCLE (in the US or Canada), or
your local distributor (outside the
US or Canada).
Faults have been detected in
Call (888) MJ CYCLE (in the US
sensors in the heat sink and
5 HS/PS-SF-PT power supply. To prevent or Canada), or your local
distributor (outside the US or
overheating, the program has
Canada).
been automatically stopped.
An irregularity has been
detected in a heat sink sensor.
23,21, or 20 HSSF The sensor will be checked and No action required at this time.
you will be notified if any
problem is found.

10-4
 Troubleshooting

Remote Error Code Reason Action

Error Code
Call (888) MJ CYCLE (in the US
The internal fan is not providing
or Canada), or your local
7 IFF adequate cooling for the
distributor (outside the US or
instrument.
Canada).
An irregularity has been
detected in a heated lid sensor.
The heated lid has been
22 LSF temporarily turned off. The No action required at this time.
sensor will be checked and you
will be notified if any problem is
found.
An imbalance has been Call (888) MJ CYCLE (in the US
None LRPI detected in the sample block. or Canada), or your local
There may be a problem with a distributor (outside the US or
Peltier module. Canada).
Call (888) MJ CYCLE (in the US
A memory fault has been found.
or Canada), or your local
None MC Stored programs may be
distributor (outside the US or
affected.
Canada).
Please delete unused programs,
or call (888) MJ CYCLE (in the
None NMA All available memory has been
US or Canada), or your local
filled.
distributor (outside the US or
Canada).
A possible fault was detected in Check probe and connections.
the in-sample probe. The If problem reoccurs please call
thermal control method has (888) MJ CYCLE (in the US or
18 PSF
been switched to Calculated Canada), or your local distributor
Mode. Results may have been (outside the US or Canada).
affected.
Please observe the following
guidelines: 1) place instruments
at least 10cm apart, 2) avoid
placing instruments in any
location where hot air might
enter the intake vents, 3) place
instrument on a hard surface with
The power supply temperature is no debris or paper underneath,
somewhat higher than normal. 4) clean all air vents and Alpha
9 PSO-CAF The power supply sensor will be unit fins of dust and debris, 5)
checked and you will be avoid running the instrument in
notified if any problem is found. areas with ambient temperatures
above 25°C. Continue to use the
instrument. If problem reoccurs
please call (888) MJ CYCLE (in
the US or Canada), or your local
distributor (outside the US or
Canada).

10-5
 DNA Engine Dyad Operations Manual

Remote Error Code Reason Action

Error Code
Please observe the following
guidelines: 1) place instruments
at least 10cm apart, 2) avoid
placing instruments in any
location where hot air might
The power supply temperature enter the intake vents, 3) place
was higher than normal. To instrument on a hard surface with
prevent instrument damage, the no debris or paper underneath,
program was automatically 4) clean all air vents and Alpha
3 PSO-PT
stopped. Overheating may be unit fins of dust and debris, 5)
caused by inadequate airflow or avoid running the instrument in
a problem with the power areas with ambient temperatures
supply. above 25°C. Do not use the
instrument until you call (888) MJ
CYCLE (in the US or Canada), or
your local distributor (outside the
US or Canada).
An irregularity was detected in
a power supply temperature
15 PSSF sensor. The sensor will be No action required at this time.
checked and you will be
notified if any problem is found.
Please observe the following
guidelines: 1) place instruments
at least 10cm apart, 2) avoid
placing instruments in any
location where hot air might
enter the intake vents, 3) place
The block took slightly longer
instrument on a hard surface with
than expected to achieve the
no debris or paper underneath,
programmed temperature. This
4) clean all air vents and Alpha
12 SBC-CAF condition may be caused by
unit fins of dust and debris, 5)
inadequate airflow, or a
avoid running the instrument in
problem with the Alpha unit
areas with ambient temperatures
itself.
above 25°C. Continue to use the
instrument. If problem reoccurs
call (888) MJ CYCLE (in the US
or Canada), or your local
distributor (outside the US or
Canada).
The heated lid took slightly Call (888) MJ CYCLE (in the US
longer than expected to reach or Canada), or your local
13 SLC its target temperature. There distributor (outside the US or
may be a problem with the lid Canada).
sensor or lid heater.

10-6
 Troubleshooting

Remote
Error Code Reason Action
Error Code
A program containing a If you place a 96-well Alpha unit
None GPA gradient step can only be run in this quadrant, you may run
on a 96-well Alpha unit. this gradient program.
The program entered may only
run in Calculated or Block
temperature control mode. No action required. Temperature
Probe mode is unavailable for mode has been automatically
None CCM this type of program. For switched to Calculated control for
optimum results, the temperature this run only.
control mode has been
automatically switched to
Calculated control.
The thermal gradient has not
Call (888) MJ CYCLE (in the US
been achieved as quickly as
25 GF or Canada), or your local
expected. This may indicate a
distributor (outside the US or
possible problem with the
Canada).
Alpha unit.
Replace fuse on instrument and
The instrument has detected confirm that instrument is
unexpected temperature functional. If problem reoccurs
10 UF please call (888) MJ CYCLE (in
readings. This may indicate a
problem with the Alpha unit. the US or Canada), or your local
distributor (outside the US or
Canada).
Call (888) MJ CYCLE (in the US
A ground fault was detected in or Canada), or your local
26 None
an Alpha unit. distributor (outside the US or
Canada).
Call (888) MJ CYCLE (in the US
A problem was detected in a or Canada), or your local
27 None
Power Bonnet lid. distributor (outside the US or
Canada).

10-7
 DNA Engine Dyad Operations Manual

Problems in Power-Up
Should a Dyad cycler not power up properly, as indicated in Chapter 4, please follow the
steps outlined in the flowchart (figure 10-1) to determine the best course of action. In this
case, a problem should be consistent and repeatable.

Figure 10-1: Power-up Troubleshooting Flowchart

Turn power on

y n
Is t he f an on?

Plug cycler into n

Is uni t plugged In?
220Vac
Did you h ear n
a "b eep"?
y
y

Are Alpha units in

Secure Alpha n the correct position,
units and are handles locked
in place?

Does t he initialization n
screen appear?
Replace f uses n Are f uses
5x20mm 6.3A good?

y
y

Unit defective-
return for service

Was '1' hit y

Self t est
to enter Selftest?

n
y n
Pass?

Does the
'About' screen n
appear?

y
Unit ready

10-8
 Troubleshooting

Problems with System Performance

Should you encounter problems with menu navigation, front panel manipulation, or any
performance aspect of a Dyad cycler that has successfully powered up, please follow the
steps in this flowchart to determine the best course of action. Again, a problem should be a
consistent, repeatable problem.

Figure 10-2: System Performance Troubleshooting Flowchart

Unit r eady

Select 1st block

Re-boot and run self-

test program

Are temperatures n
indicated
on the display?
y
Pass?

y
n
Front-end software may have
become corrupted.
Select last b lock Re-load software.
Re-Test.

Are temperatures n Problem y

indicated
corrected?
on the display?

y
Unit defective-
r eturn for service

Static checks?

Are the number keys working? (Try an Instant Incubate.)

Are the cursor keys working? (Try navigating a window with them.)
Is the touch pad working? (Move the c ursor. Hit the 'CLICK' button.)
Is the touch pad/mouse selection switch in the appropriate position? (Rear position
for touch pad function or forward position for mouse function.)
Does the external mouse port function?
Front- end OK ;
proceed

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 DNA Engine Dyad Operations Manual

Problems with an Alpha Unit

An Alpha unit is a distinct, separately engineered piece of equipment that is made to inter-
face with all MJ Research DNA Engine line thermal cyclers. However, to rule out problems
with any Alpha unit, please follow this recommended troubleshooting flowchart.

Figure 10-3: Alpha Unit Troubleshooting Flowchart

System status at this p oint:

Front- end OK ; front-end OK, communicating w/ engines.
proceed Problem: protocols do not a ppear to be
running properly.

Check error l og

Is problem Alpha Alpha unit defective;

unit related? return for service

Base defective;
r eturn for service

Problems Related to Protocols

The suggestions we make here are by no means exhaustive, but are intended as a starting
point for further investigation. Should the Dyad system check out OK, we recommend posi-
tive controls for troubleshooting purposes.

Following is a general description of some common problems related to the protocols and
reaction components in sequencing and thermal cycling applications. For a more detailed
discussion of protocols and reactions, see Current Protocols in Molecular Biology (F. Ausubel
et al., eds., John Wiley & Sons)

10-10
 Troubleshooting

Problem Cause Action

No reaction products Wrong protocol used. Re-run reaction using correc t
obtained. protocol.
Protocol contains a wrong value. Use List utility to check proto-
col's temperature control meth-
od, temperatures, and times.
Reaction component omitted from Check reaction assembly proto-
mixture. col, ensuring that mixture con-
tains appropriate components
in correct concentrations.
Denaturation temperature too Use >92° C for denaturation.
low. Only rarely are temps higher
than 94°C required, however.

Annealing temperature too high Check for appropriate anneal-

for primers. ing temperatures of primers,
using available computer pro-
grams or empirical testing.
Wrong temperature control Use List utility to check
method used. temperature control method for
protocol; change if needed.
Probe failed, causing machine to Check screen for probe failure
run protocol under calculated error message. Probe may need
control. servicing or replacing. Call MJ
Re s earc h, Inc. or your local
distributor.
Probe not filled with correct Fill probe tube with correct
amount of oil. amount of oil (see p. 4-12).
Reaction mix contains an inhibitor Test a complete reaction mix,
(e.g., heme from blood). minus sample, with a control
template and primer set.
Reaction vessels not making good Use only high-quality
thermal contact with sample tubes/plates that fit block
block. snugly. Ensure that wells are
free of foreign materials that
would interfere with tube/plate
seating.

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 DNA Engine Dyad Operations Manual

Table 10-2: Protocol Difficulty

Error Message Cause and Result Action

Reaction is working "Primer-dimer" material often If obtaining appropriate reac-
but broad low mole- produces a broad band in the tion product/s, no need to
cular weight band is <100bp region of gels. change anything.
seen in gels.
Minimize "primer-dimer"
production by designing
primers with no 3' self-
complementarity.
Reoptimize magnesium concen-
tration and annealing temper-
ature to maximize desired pro-
duct and minimize "primer-
dimers."
Reaction working but Nonspecific hybridization occur- Program a hot start into the
unexpected extra ring during setup. protocol.
products or smear is
seen.
Reaction component concentration Check concentratons of compo-
too high or too low. nents. May need to reoptimize
magnesium concentration.
Annealing temperature too low. Reoptimize annealing
temperature.
Protocol contains a wrong value. Use List utility to check proto-
col's temperature control
method, temperatures, and
times.
Template not of sufficient purity. Check extraction and purifi-
cation protocols. Add additional
purification steps if necessary.
Multiple templates or host DNA Check nucleic acid preparations
in sequencing reactions. by gel electrophoresis.

10-12
 Troubleshooting

Problems due to Environmental Conditions, Setup,

and Maintenance
Strict adherence to the installation, operation, and maintenance instructions provided in
Chapters 3, 4, and 9 are tantamount to the continued trouble free operation of the Dyad
cycler. Should it be determined that the source of a problem is due to incorrect operation or
setup, consult Table 10-3 for a list of problems and suggested solutions.

Table 10-3: Environmental difficulties

Problem Cause Action

Frequent shutdowns Machine is not receiving enough Make sure air intake vents are
due to overheating. air. not obstructed by dust, debris,
Frequent "Slow Block or paper. Remove light collec-
Cycling," "HS tions of dust and debris with
Overheat," and "HS damp cloth. Vacuum out heavy
Overheating" error collections. Remove any papers
messages. placed under the machine. Posi-
tion machine at least 10cm from
vertical surfaces.
Air flowing into intake vents is Check temperature of air enter-
not < 31° C. ing air intake vents, following
procedure on p. 3-4. If higher
than 31° C , use Table 3-1 to
troubleshoot and remove
cause/s.
Dust and debris clog- Failure to regularly check for Remove light collections with
ging up air intake buildup. damp cloth. Vacuum out heavy
vents. collections.

10-13
 DNA Engine Dyad Operations Manual

10-14