Package Component - FAQs

You may, but W2 may run out in the middle of the second run. However, you can collect the data right before W2 runs out and reanalyze it after the run finishes. If you want complete data, please perform only one run per initialization.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

If you are using the Ion PGM™ 200 Sequencing Kit v2, you can perform a run within 27 hours after initialization. If you are going to perform two runs, make sure the second one starts within 27 hours.

If you are using the Ion PGM™ 200 Sequencing Kit, the limit is shorter; you will need to perform a run within 10 hours.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The touchscreen shows the voltage measured on the chip and there will be some contrast according the signal intensity which may look like bubbles.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The pH may not have been properly measured or the volume of W3 may be too small. Please check the following:

1) That there is 50 mL of solution inside the W3 bottle
2) That the sippers and bottles attached to the instrument are not loose
3) That the color of the sippers on the instrument are gray and blue

If there is not enough W3, please add more until it reaches the 50 mL line on the bottle.

If you are accidentally using the dark blue sippers (for the dNTPs), the tip will not touch the solution, since it is too short. Replace the sippers, press the 'start' button, and if the same message appears, change the chip to a different one and try again.

If you get an error, shut down and restart the Ion PGM System. Discard the solution inside the W1 bottle, make new solution by adding 350 ul of 100 mM NaOH, and restart initialization.

Also, if you are using an Ion 316 Chip v2 on a v3.4 or older instrument, the instrument will not recognize the chip.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

Please check the following:
1) That there is solution left in the W1 bottle
2) That the sippers and bottles are not loose

If the sippers and bottles are not loose and there is at least 200 mL of solution in the W1 bottle, the line between W1 and W2 may be blocked. Please run the line clear.

If the same error message appears even after the line is clear, detach the reagent bottles from the Ion PGM System, water clean and shut down the instrument. Cap the reagent bottles. Restart the instrument and check the Ion PGM chip. Open the chip clamp and check that there is no solution standing in the port of the chip. If there is some solution, change the chip to another used chip or a new chip.

Place the W2 and W3 bottles back on the Ion PGM System. Discard the solution inside the W1 bottle, make more solution by adding 350 µL of 100 mM NaOH, and place it back on the Ion PGM System. Restart initialization.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The Ion PGM System and Torrent Server may not be connected. Please shut down the system and server and reboot them. The server may enter a system check after the reboot. Since the system check will take 3-4 hours, you can avoid it by pressing the 'c' button on the keyboard.

If there is a reason you cannot reboot the system, you can run the Ion PGM System without connection to the server. The runs will be saved inside the system. For 200 bp sequencing, this many runs can be saved inside the system:
314 chip: 40 runs
316 chip: 6 runs
318 chip: 5 runs

The data will automatically transfer to the server after connection.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The pH of W1 may be out of range or the volume of W1 may be too small or there may have been a minor problem during measurement. Check the amount of W1, press the 'Start' button on the screen, and restart the measurement. If it passes, continue to start the run. If an error appears again, please note the pH of W1, the amount of W1, as well as the error message, and contact Technical Support.br/>
Please note that passing pH values for the reagents may vary depending on the sequencing kit used, but the instrument will automatically determine the correct pH range depending on the sequencing kit selected during initialization. If you are performing the reagent check outside of the initialization, please contact Technical Support for guidance.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.

The pH of the nucleotides may be out of range or there may have been a minor problem during measurement. Press the 'Start' button and restart the measurement. If it passes, continue to start the run. If an error appears again, please note the pH of R1, R2, R3, R4, as well as the error message, and contact Technical Support.

Find additional tips, troubleshooting help, and resources within our Next-Generation Sequencing Support Center.