Troubleshooting resources

For more troubleshooting information, see the instrument user guides on the Ion S5™ System, Ion S5™ XL System, and Ion GeneStudio™ S5 System product pages. You can also search for manuals on the Services & Support tab at www.thermofisher.com.

  • Customer Support Archive (CSA)—For problems that require technical help, obtain the CSA. The sequencing CSA is used by Technical Support to diagnose problems. Due to the large size of the full analysis CSA, it is necessary to use the thumbnail version for troubleshooting purposes. To download this CSA:

    1. In the Data tab, click Completed Runs & Reports, then click the Report Name link with "_tn" appended.

    2. In the left navigation menu, click Details, or scroll to the Details section of the run report, then click the Support tab.

    3. Click Download to download a compressed directory that contains a PDF and HTML version of the run report, and logs that can be used for troubleshooting.

    4. Email the report to Technical Support. If you would like to be able to upload these support files directly, ask your local Field Service Engineer how to enable the Customer Support Archive function.

  • Instrument log files—Instrument log files from the Ion OneTouch™ 2 or Ion Chef™ instruments can also be sent to Technical Support for troubleshooting help. Contact Technical Support for instructions to download instrument log files. The CSA includes instrument log files.

  • Turn off 3' quality trimming—In cases of shorter-than-expected library reads, the 3’ quality trimming can be turned off to help distinguish short reads that originate from the library preparation and short reads resulting from the 3’ quality trimming by the software. To turn off the 3’ quality trimming:

    1. In the Data tab, click Completed Runs & Reports.

    2. Search, filter, or sort the list to find your run report of interest.

    3. In Table View mode, in the row of the run of interest, click (Actions) > Reanalzye.

    4. Under the Advanced options, on the Start reanalysis from line, select Base Calling.

    5. In the Basecaller args field, change the --trim-qual-cutoff 15 value to 100. The field should now read, BaseCaller --trim-qual-cutoff 100 --trim-qual-window-size 30 --trim-adapter-cutoff 16.

    6. Give the reanalysis report a new name and select Start Analysis.

  • ISP QC (Qubit™ data)

  • Library QC data (Agilent™ Bioanalyzer™ Instrument trace or quantification data)

  • Ion Library, Template Kit, and Sequencing Kit names and lot numbers

Related Topics
Parent topic: Troubleshooting