Thermo Scientific Ion GeneStudio S5 User Manual Download Page 41

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Troubleshooting using control libraries

Observation

Possible cause

Recommended action

Ion Sphere

™

Test Fragments

are not present in the Test

Fragment Report section of the

run report, and library

sequencing is poor

• Chip loading was poor.
• Control Ion Sphere

™

Particles were not added

to the sample

1. Confirm that the Control Ion Sphere

™

Particles (included in the Ion S5

™

Installation Kit) were added.

2. If controls were added, contact Technical

Support.

Control Ion Sphere

™

Particles

are present in the run report,

but AQ20 throughput is poor

• The quality of the library

was poor.

• The quality of the template

preparation was poor.

Verify the quality of the library and template

preparations using quality assessment

procedures recommended in the appropriate

library and template preparation user guides.

1. Use the Human CEPH Genomic DNA

Control or Human CEPH Control 200

Library, included in the Ion S5

™

Controls

Kit (Cat. No. A27760), to prepare

template-positive ISPs with the Ion Chef

™

Food Protection Instrument.

2. Use the ISPs in an Ion GeneStudio

™

Food Protection Instrument run.

3. If AQ20 throughput is still below

specification, verify the quality of

unenriched and enriched ISPs to identify

a problem in template preparation.

4. If ISP quality is good, but AQ20 throughput

is below specification, contact Technical

Support.

Solid-state buffer leak

Observation

Possible cause

Recommended action

Two or more of the following

observed

• Excessive read trimming

or the number of short

reads is significantly

higher than expected.

• Percentage of low quality

reads is significantly

higher than expected.

• Poor sequencing

performance or no Test

Fragments.

A solid-state buffer leak

occurred.

Contact Technical Support.
Perform the pulse cleaning protocol if directed

to do so by Technical Support or your Field

Service Engineer (FSE).

Appendix B

Troubleshooting

Troubleshooting using control libraries

Ion GeneStudio

™

S5 Food Protection Instrument User Guide

Summary of Contents for Ion GeneStudio S5

Page 1: ...For testing of Food and Environmental samples only Ion GeneStudio S5 Food Protection Instrument USER GUIDE Catalog Numbers A39513 Publication Number MAN0017965 Revision A 0 ...

Page 2: ... S WILL NOT BE LIABLE FOR SPECIAL INCIDENTAL INDIRECT PUNITIVE MULTIPLE OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT INCLUDING YOUR USE OF IT Revision history Pub No MAN0017965 Revision Date Description A 0 18 October 2018 New document Trademarks All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified 2018 Thermo Fish...

Page 3: ...GeneStudio S5 Food Protection Instrument input and output connections 11 CHAPTER 3 Instrument operation 12 Power the Ion GeneStudio S5 Food Protection Instrument on or off 12 Power on 12 Power off 12 Update the Ion GeneStudio S5 Food Protection System software 12 Instrument run times 13 Maintain the Ion GeneStudio S5 Food Protection Instrument 14 Materials required 14 Clean or decontaminate the in...

Page 4: ...ate buffer leak 41 Pulse clean the Ion GeneStudio S5 Food Protection Instrument 42 APPENDIX C Instrument warranty 43 APPENDIX D Safety 45 Safety alerts on this instrument 45 Location of safety labels on the instrument 46 Safety information for instruments not manufactured by Thermo Fisher Scientific 46 Instrument safety 47 General 47 Cleaning and decontamination 47 Electrical safety 48 Safety and ...

Page 5: ... in this document IMPORTANT Before using this product read and understand the information in the Safety appendix in this document Purpose of the guide This Ion GeneStudio S5 Food Protection Instrument User Guide Pub No MAN0017965 provides reference information for using and maintaining the Ion GeneStudio S5 Food Protection System Cat No A39513 Ion GeneStudio S5 Food Protection Instrument User Guid...

Page 6: ...Reagents OT2 A27897 1 Ion S5 Cartridge Tool A28308 2 15 C to 30 C Ion Chef S5 Series Chip Balance A29022 1 Optional materials and equipment Unless otherwise indicated all materials are available through thermofisher com MLS Fisher Scientific fisherscientific com or other major laboratory supplier Item 1 Source Optional Non interruptible Power Supply UPS 2 MLS 1 IMPORTANT Thermo Fisher Scientific h...

Page 7: ...tory or work area Instrument vibration and clearances IMPORTANT Significant vibration during sequencing may add noise and reduce the quality of the measurements The Ion GeneStudio S5 Food Protection System must be installed on a bench that is free from vibrations or in contact with equipment that can cause vibrations to the bench freezers pumps and other similar equipment IMPORTANT Place the instr...

Page 8: ... Ion GeneStudio S5 Food Protection Instrument 2 Ion Chef Food Protection Instrument 3 Local area network 4 Internet 5 Client computer Note The Ion Chef Food Protection Instrument must be connected to the Torrent Server either directly using a category 6 Ethernet cable or indirectly through a local area network that has been configured to allow HTTP 443 SSH 22 and FTP 20 21 traffic 2 8 Ion GeneStud...

Page 9: ...ction System warranty or any service contract you may have bought You are required to schedule an on site Time and Materials visit by a field service engineer to correct the problem at your own expense In providing outbound access to the Internet from the server you enable the support team to provide inbound support The Ion GeneStudio S5 Food Protection Instrument runs a remote monitor agent that ...

Page 10: ...ng Solution bottle 7 Waste reservoir Note The system uses RFID technology to verify that the proper reagents are loaded in positions 3 5 and 6 Reagents that exceed their expiration date or usage count generate an error message prompting the user to replace the reagent before performing the run Note RFID regulatory information can be found on the main screen under Options4Regulatory info Chapter 2 ...

Page 11: ... and a local area network 3 Ethernet port An RJ45 port that provides Ethernet gigabit communication with the Ion Chef Food Protection Instrument 4 On off switch Power switch where the states are on or off O 5 Power port 100 240VAC port that provides power to the instrument Chapter 2 System components Ion GeneStudio S5 Food Protection Instrument input and output connections 2 Ion GeneStudio S5 Food...

Page 12: ...s 1 In the Main Menu press Settings4System Tools4Shut Down 2 Select either Shut Down or Reboot Note If you select Shut Down a confirmation message appears Select Yes to power off the instrument Note Do not press the power button during a run Interrupting power to the instrument during a run may result in sequencing run failure and loss of sample Update the Ion GeneStudio S5 Food Protection System ...

Page 13: ...n time is shorter for this application Chip type Number of reads Read length output Instrument run time Ion GeneStudio S5 Food Protection Instrument Ion 510 Chip 2 3 M 200 bases 0 3 0 5 Gb 4 5 hours 400 bases 0 6 1 Gb 10 5 hours Ion 520 Chip 4 6 M 200 bases 0 6 1 Gb 7 5 hours 400 bases 1 2 2 Gb 12 hours 3 4 M 600 bases 0 5 1 5 Gb 12 hours Ion 530 Chip 15 20 M 200 bases 3 4 Gb 10 5 hours 400 bases ...

Page 14: ...Enable post run clean checkbox for the first sequencing run The post run cleaning is then performed normally after the second sequencing run However if the Enable post run clean checkbox is deselected for the second run the cleaning is not performed after either run If the second sequencing run is not performed or the cleaning is not performed automatically after the second run the instrument will...

Page 15: ...y installed IMPORTANT Perform the cleaning with a used reagent cartridge and wash solution bottle installed The cleaning procedure pumps cleaning solution into the wash solution bottle and reagent cartridge making them unsuitable for sequencing 5 Place a used sequencing chip in the chip clamp then push the chip clamp in all the way to engage 6 Close the instrument door then press Next Cleaning tak...

Page 16: ...g procedure before reinitialization 1 In the instrument touchscreen main menu touch Run The instrument door unlocks and the chip clamp disengages 2 Ensure that a used sequencing chip is in the chip clamp then push the chip clamp in all the way to engage 3 Close the instrument door then touch Next 4 When prompted select Planned Run none Ensure that the Enable post run clean checkbox is selected the...

Page 17: ...rmed automatically at the completion of the previous sequencing run Perform a Clean if for any reason the sequencing run was not properly completed Follow the instructions that are provided on the touchscreen The Initialize program must be performed before each run to load and prepare the run reagents The Initialize program walks you through Emptying the waste reservoir Loading the reagent cartrid...

Page 18: ...ns and update the installed software Note The Service tools option is for use by trained service personnel only Use the Network Settings menu to configure IP address Torrent Server and FTP settings Network Settings Appendix A Touchscreen reference Settings A 18 Ion GeneStudio S5 Food Protection Instrument User Guide ...

Page 19: ...t to activate the field A virtual keyboard appears 3 Enter the new information then press Done Torrent Server Configuration Change the Torrent Server IP address and user information Enter the IP addresses in the TSUrl field When a change to the Torrent Server IP address or user information is required Appendix A Touchscreen reference Settings A Ion GeneStudio S5 Food Protection Instrument User Gui...

Page 20: ...n is required Update Server Update the software update server Enter the IP address in the UpdateUrl field When a change to the URL for the software server update is required The values on this screen are set at installation Do not change the settings except at the direction of Thermo Fisher Scientific service staff Appendix A Touchscreen reference Settings A 20 Ion GeneStudio S5 Food Protection In...

Page 21: ...ct expiration date and remaining uses of the product To determine if reagents that were left on an instrument during a period of instrument shutdown have expired 1 Press the screen within the row of the product to view an RFID Tag Detail page 2 Press Done to return System Tools Appendix A Touchscreen reference Settings A Ion GeneStudio S5 Food Protection Instrument User Guide 21 ...

Page 22: ...rt Chip Calibration Checks the status of a chip 1 Insert a chip into the chip clamp 2 Press Chip Calibration to start the chip calibration 3 In the dropdown lists select the Image to display and the type of Calibration to perform 4 Press Cancel to quit the chip calibration Appendix A Touchscreen reference Settings A 22 Ion GeneStudio S5 Food Protection Instrument User Guide ...

Page 23: ...eck for an Ion 550 Chip If directed to do so by Technical Support as part of a troubleshooting procedure Press Run to start the reagent check Press Last Trace to review the most recent reagent check result trace Note Reagent Check confirms that the chip calibration passes and will only fail if the chip is defective or Ion S5 Wash Solution is not flowing Appendix A Touchscreen reference Settings A ...

Page 24: ... The Filesystems screen opens 2 Press the screen within the row of the Filesystem you want to view then press Details The Disk Drives in Filesystem screen opens 3 Press the screen within the row of the Drive to view details of the disk drive The Details for Drive screen opens 4 Press Done to return to the previous screen Appendix A Touchscreen reference Settings A 24 Ion GeneStudio S5 Food Protect...

Page 25: ...then press Next The pulse cleaning procedure starts automatically Upload Diagnostics Allows upload of instrument diagnostics files for review by support personnel For troubleshooting if directed to do so by Technical Support Note The system must be connected to an active network port If no network is present the file is pushed to the Torrent Browser You can then download the file and email it to T...

Page 26: ... do so by Technical Support as part of a troubleshooting procedure When software updates are available users will receive a Notification through the home screen 1 In the Settings menu press Check for Updates The Software Update screen lists the available updates 2 Press Update to automatically download and install the updates Check for software updates Appendix A Touchscreen reference Settings A 2...

Page 27: ...instrument If the instrument hard drive becomes full see Manually delete run data on page 29 Transfer data Transfer run data from the instrument hard drive to the Torrent Server 1 Touch the screen in the Experiment Name row of the individual experiment to be transferred 2 Press Transfer 3 Select the radio button of the action to be performed 4 Select the radio button of the files to be transferred...

Page 28: ...he Experiment Name row of the individual experiment to be analyzed then press Analysis 2 Select the Stop Analysis or Restart Analysis radio button then press OK 3 If performing a re analysis follow the on screen instructions then press OK Appendix A Touchscreen reference Settings A 28 Ion GeneStudio S5 Food Protection Instrument User Guide ...

Page 29: ...leted from the instrument hard drive 1 In the Settings menu press Data Management to access the Data Management screen then press Manage 2 Press Select All to select all the available experiments or touch the screen in the Experiment Name row of the individual experiment to be managed 3 Press Delete Selected Manually delete run data Appendix A Touchscreen reference Settings A Ion GeneStudio S5 Foo...

Page 30: ... was not completed IMPORTANT Do NOT perform a manual cleaning with an unused initialized Ion S5 Wash Solution cartridge Perform an instrument reset run instead See Perform an instrument reset run with an initialized unused Ion S5 Wash Solution cartridge on page 16 for more information 1 In the Settings menu press Clean Instrument 2 Follow the on screen instructions see Manually clean the instrumen...

Page 31: ...plete The Instrument Settings menu provides information about the instrument and allows you to set the instrument name and calibrate the touchscreen Instrument settings Appendix A Touchscreen reference Settings A Ion GeneStudio S5 Food Protection Instrument User Guide 31 ...

Page 32: ...nformation or access regulatory information Regulatory Info Lists instrument specific regulatory information To view instrument regulatory information Instrument Name To change the instrument name Appendix A Touchscreen reference Settings A 32 Ion GeneStudio S5 Food Protection Instrument User Guide ...

Page 33: ...or a stylus each time it appears In total you will touch the screen 4 times one time in each corner Language To set the user interface language Set to customer preference during instrument installation Touchscreen icons 1 1 1 4 3 2 5 6 7 8 9 Appendix A Touchscreen reference Touchscreen icons A Ion GeneStudio S5 Food Protection Instrument User Guide 33 ...

Page 34: ...ms If the alarm persists contact Technical Support 7 Chip block temperature Good Chip block temperature Bad If the icon reads 0 and there is an alarm contact Technical Support 8 Instrument File System Space the percent of file space used is indicated 1 The instrument checks for sufficient disk space before each run and notifies the user if there is not enough 9 Torrent Server File System Space the...

Page 35: ...ve that failed Indicates that a drive is failing Failed to mount the results filesystem One or more drives are missing from the RAID that makes up sw_results System sensor check failed ipmi sensors A component on the motherboard is failing or has failed System sensor check failed CC CC V LL LL HH HH Where CC CC current voltage LL LL the low voltage threshold HH HH the high voltage threshold Indica...

Page 36: ...g or has stopped working Nonfatal alarms Instrument must be cleaned before starting another run Maximum number of runs since last clean has been exceeded Perform an instrument cleaning see Manually clean the instrument on page 14 Ambient temperature is above the threshold of 35 C Verify the temperature in the lab Contact Technical Support if the temperature of the lab is within normal operating te...

Page 37: ...tection Instrument input and output connections on page 11 for the Ethernet port location If the problem persists contact Technical Support Newer Software Available Notification that software updates are available Update your software See Check for software updates on page 26 Appendix A Touchscreen reference Alarms Notifications and Events A Ion GeneStudio S5 Food Protection Instrument User Guide ...

Page 38: ...allation is complete follow the onscreen prompts to restart the instrument Note Sometimes the instrument restarts automatically after software installation If a message states No Connectivity to Torrent Server No Connectivity to ftp server or Network Manager not connected disconnect and reconnect the Ethernet cable confirm that the router is operational and verify that the network is up and runnin...

Page 39: ...he chip fails replace it with a new chip then press Chip Check 5 If Chip Check continues to fail there could be a problem with the chip socket Contact Technical Support Reagent Check fails A chip failure was detected 1 Replace the used sequencing chip used during initialization with a different used chip 2 Press Retry 3 If the initialization completes without failure touch Home then continue with ...

Page 40: ... Check continues to fail contact Technical Support Ensure that you install the Ion S5 Wash Solution bottle with the instrument door fully open If you install the bottle impeded by a partially closed door the port can be obstructed and a faulty installation and wash failure can result Bottle leak check fails Bottle seal was not tight Bottle was damaged or defective 1 Finger tighten the bottles 2 If...

Page 41: ...y included in the Ion S5 Controls Kit Cat No A27760 to prepare template positive ISPs with the Ion Chef Food Protection Instrument 2 Use the ISPs in an Ion GeneStudio S5 Food Protection Instrument run 3 If AQ20 throughput is still below specification verify the quality of unenriched and enriched ISPs to identify a problem in template preparation 4 If ISP quality is good but AQ20 throughput is belo...

Page 42: ...leaning before a pulse cleaning can be performed see Manually clean the instrument on page 14 Initialize Instrument is ready to be pulse cleaned Proceed to step 2 2 Press Settings 4System Tools4Pulse clean 3 Follow the onscreen prompts to prepare the instrument Install new bottles of Ion S5 Cleaning Solution in both the Wash and Cleaning solution positions Replace the Ion S5 Sequencing Reagents ca...

Page 43: ...n Torrent Product directly from Life Technologies are not transferable and do not extend to the benefit of any other person or entity unless otherwise expressly stated in writing by Life Technologies ANY PRODUCT NOT COVERED BY AN EXPRESS WRITTEN WARRANTY IS SOLD AND PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND STATUTORY EXPRESS OR IMPLIED Any description of Ion Torrent Product recited in Life Techn...

Page 44: ...LUDING WITHOUT LIMITATION ANY CLAIM OF INACCURATE INVALID OR INCOMPLETE RESULTS WHETHER ARISING FROM A STATUTE OR OTHERWISE IN LAW OR FROM A COURSE OF PERFORMANCE DEALING OR USAGE OF TRADE Appendix C Instrument warranty Solid state buffer leak C 44 Ion GeneStudio S5 Food Protection Instrument User Guide ...

Page 45: ... gowns eye protection and so on To obtain SDSs see the Documentation and Support section in this document Safety alerts on this instrument Additional text may be used with one of the symbols described above when more specific information is needed to avoid exposure to a hazard See the following table for safety alerts found on the instrument English Français CAUTION Hazardous chemicals Read the Sa...

Page 46: ...ry symbols Ion GeneStudio S5 Food Protection Instrument label Safety information for instruments not manufactured by Thermo Fisher Scientific Some of the accessories provided as part of the instrument system are not designed or built by Thermo Fisher Scientific Consult the manufacturer s documentation for the information needed for the safe use of these products Location of safety labels on the in...

Page 47: ...rer users should confirm with the manufacturer that the proposed method will not damage the equipment MISE EN GARDE Nettoyage et décontamination Utiliser uniquement les méthodes de nettoyage et de décontamination indiquées dans la documentation du fabricant destinée aux utilisateurs L opérateur ou toute autre personne responsable est tenu d assurer le respect des exigences suivantes Ne pas utilise...

Page 48: ...la terre est déconnecté La continuité de la mise à la terre est impérative pour le fonctionnement de l instrument en toute sécurité WARNING Power Supply Line Cords Use properly configured and approved line cords for the power supply in your facility AVERTISSEMENT Cordons d alimentation électrique Utiliser des cordons d alimentation adaptés et approuvés pour raccorder l instrument au circuit électr...

Page 49: ...ry use Part 2 010 Particular requirements for laboratory equipment for the heating of materials Reference Description Directive 2014 30 EU European Union EMC Directive EN 61326 1 Electrical Equipment for Measurement Control and Laboratory Use EMC Requirements Part 1 General Requirements AS NZS CISPR 22 2009 A1 2010 Limits and Methods of Measurement of Electromagnetic Disturbance Characteristics of...

Page 50: ...er Scientific can void your authority to operate this equipment under Federal Communications Commissions rules Canada This device complies with Industry Canada licence exempt RSS standard s Operation is subject to the following two conditions 1 this device may not cause interference and 2 this device must accept any interference including interference that may cause undesired operation of the devi...

Page 51: ...ry the waste generated by the particular applications reagents and substrates used in your laboratory Ensure that the waste is stored transferred transported and disposed of according to all local state provincial and or national regulations IMPORTANT Radioactive or biohazardous materials may require special handling and disposal limitations may apply AVERTISSEMENT PRÉCAUTIONS GÉNÉRALES EN CAS DE ...

Page 52: ... nationales et communautaires en matière de confinement des récipients Une fois le récipient à déchets vidé il doit être refermé hermétiquement avec le couvercle fourni Caractériser par une analyse si nécessaire les déchets générés par les applications les réactifs et les substrats particuliers utilisés dans le laboratoire Vérifier que les déchets sont convenablement stockés transférés transportés...

Page 53: ... Food Safety support Website thermoscientific com foodmicro or thermofisher com foodsafety Support email Europe Middle East Africa microbiology techsupport uk thermofisher com North America microbiology thermofisher com Phone Visit thermofisher com support select the link for phone support and select the appropriate country from the dropdown menu Ion GeneStudio S5 Food Protection Instrument User G...

Page 54: ...thermofisher com support thermofisher com askaquestion thermofisher com 18 October 2018 ...

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