Spatial Calibration Troubleshooting - Thermo Scientific appliedbiosystems SeqStudio Flex Series User Manual

Appendix A Troubleshooting
A

Spatial calibration troubleshooting

Observation
Sample data files from the instrument can be
opened but not analyzed in secondary analysis
software
• Sequencing Analysis Software
• SeqScape ™
Software
• Variant Reporter ™
Software
• Minor Variant Finder Software
• MicrobeBridge Software
• GeneMapper ™
Software
Files cannot be imported into Thermo Fisher
Connect applications or cannot be analyzed in
Thermo Fisher ™ Connect sequencing apps

Spatial calibration troubleshooting

Observation
Spatial and spectral calibration
reports list original date of
capillary array installation (not
the date of re-installation)
Persistently bad spatial
calibration results
Unusual peaks or a flat line for
the spatial calibration
522
An updated version of the
secondary analysis software
is required.
™
The sample name or file
name used a special
character.
Possible cause
—
The capillary array is damaged.
The capillary array window is
not properly positioned in the
detection cell (see Figure 3).
SeqStudio ™ Flex Series Genetic Analyzer with Instrument Software v1.0 User Guide
Possible cause
Recommended action
No action. Normal occurrence.
Run the Change capillary array maintenance
wizard to uninstall, then re-install the
capillary array. (In the home screen, tap
Actions4Maintenance4Maintenance
wizards4Change capillary array.)
Contact Technical Support.
Open the detection block door and manually
reposition the detection cell within the holder.
Ensure that the fastener on the detection block
door is firmly tightened. Repeat the spatial
calibration.
Run the Change capillary array maintenance
wizard to uninstall, then re-install the
capillary array. (In the home screen, tap
Actions4Maintenance4Maintenance
wizards4Change capillary array.)
If the calibration fails again, run the
Fill array with polymer maintenance
wizard. (In the home screen, tap
Actions4Maintenance4Maintenance
wizards4Fill array with polymer.)
Recommended action
Download and run the latest
version of secondary analysis
software. See "Secondary
analysis software" on
page 50.
Note: In the secondary
analysis software, the
SeqStudio ™ Flex Series
Genetic Analyzer instrument
is listed as 3600.
Rename the sample name or
file name.
Note: Special characters (/,
&, @, %) will impact file
import into Thermo Fisher
Connect applications.
™