08/14/20
When contacting Illumina Support for assistance, Illumina Support can efficiently access the relevant Instrument Performance Data via one or more of the following applications:
If your institutional policy does not allow the instrument to connect to the external network, or additional files are required by Illumina Support for investigation, send less than 50 Mb of data directly by attaching to an email. Only email attachments less than 50 Mb can be received by Illumina Support. If the files are too large to attach, contact techsupport@illumina.com and request a file transfer link to upload the files to a secure location. If your institution requires an alternative method for transferring files, provide the instructions to Illumina Support to access the files.
Investigation can be expedited if relevant files or folders, depending on the type of issue, are already collected for transfer.
A list of different files and their locations that may be requested by Illumina Support is provided below for each instrument.
iSeq 100
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Clustering failure* | SAV data | D:\Illumina\iSeq Runs\[RunFolder]\ InterOp Folder, RunInfo.xml, RunParameters.xml |
| Thumbnails | D:\Illumina\iSeq Runs\[RunFolder]\Thumbnail_Images | |
| Run quality | SAV data | D:\Illumina\iSeq Runs\[RunFolder]\ InterOp Folder, RunInfo.xml, RunParameters.xml |
| Pre-run check failure | Pre-run check logs | D:\Illumina\iSeq Pre Run Checks\Logs\PreRunLog.[Date/time].log D:\Illumina\iSeq Pre Run Checks\Reports\PreRunReport.[Date/time].csv |
| System check failures | System check results | D:\Illumina\iSeq System Checks\SystemCheckReport.[date/time] |
| Data transfer to network or BaseSpace Sequence Hub | UCS logs and accessory files | C:\ProgramData**\Illumina\UniversalCopyService |
*Clustering failure is indicated by an error observed at cycle 7 if running iSeq Control Software v1.4 or higher. If running v1.3 or lower, a cluster failure is indicated by a drop in intensity at cycle 9 and 0% PF (clusters passing filter).
**The ProgramData folder may be hidden. To un-hide files, select the View tab in the File Explorer window and make sure Hidden Items is selected.
MiniSeq
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Cycle 1 failure* | SAV data | D:\Illumina\MiniSeq Sequencing Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Focus images | D:\Illumina\MiniSeq Sequencing Temp\[RunFolder]\Images | |
| Run quality | SAV data | D:\Illumina\MiniSeq Sequencing Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Focus images (if requested) |
D:\Illumina\MiniSeq Sequencing Temp\[RunFolder]\Images | |
| Run aborted with error | SAV data | D:\Illumina\MiniSeq Sequencing Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Cycle logs | D:\Illumina\MiniSeq Sequencing Temp\[RunFolder]\Logs | |
| System check failures | System check results | D:\Illumina\SystemCheckResults\SystemCheckResultsDetails.csv File overwrites with each new check and folders for individual tests by date/time |
| Data transfer to network (for MiniSeq Control Software v1.2) |
RTA logs | D:\Illumina\MiniSeq Sequencing Temp\[RunFolder>]\Data\RTA Logs |
| Data transfer to BaseSpace Sequence Hub (for MiniSeq Control Software v1.2) |
BaseSpace Broker logs and accessory files | D:\Illumina\basespace broker |
| Data transfer to network or BaseSpace Sequence Hub (for MiniSeq Control Software v2 or later) |
UCS logs and accessory files | C:\ProgramData**\Illumina\UniversalCopyService\ |
*Cycle 1 failure is indicated by all cameras becoming disabled at cycle 1 due to an inability to detect clusters.
**The ProgramData folder may be hidden. To un-hide files, select the View tab in the File Explorer window and make sure Hidden Items is selected.
MiSeq
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Cycle 1 failure* | SAV data | D:\Illumina\MiSeq Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Run quality | SAV data | D:\Illumina\MiSeq Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Thumbnails (if requested) |
D:\Illumina\MiSeq Temp\[RunFolder]\Thumbnail_Images\L001\Cx.1 (where x = cycle number) |
|
| Run aborted with error | SAV data | D:\Illumina\MiSeq Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Cycle logs | D:\Illumina\MiSeq Temp\[RunFolder]\Logs | |
| Thumbnails (if requested) |
D:\Illumina\MiSeq Temp\[RunFolder]\Thumbnail_Images\L001\Cx.1 (where x = cycle number) |
|
| System check failures | System check results | D:\DiagResults\[date/time] |
| Data transfer to network (MCS 4.0 and later) |
UCS logs | C:\ProgramData\Illumina\UniversalCopyService |
| Data transfer to network (MCS v3.1 and below) |
RTA logs | D:\Illumina\MiSeq Temp\[RunFolder]\Data\RTA Logs |
| Data transfer to BaseSpace Sequence Hub | BaseSpace Broker logs and accessory files | D:\Illumina\basespace broker |
*Cycle 1 failure can be indicated by one of the following errors observed at cycle 1: Best focus not found; Best focus is too near edge of range; No usable signal found, it is possible clustering has failed; Through-focus peak did not exceed SNR threshold; Z Motor attempt to move outside soft limits.
NextSeq 500/550
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Cycle 1 failure* | SAV data | D:\Illumina\NextSeq Control Software Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Focus images | D:\Illumina\NextSeq Control Software Temp\[RunFolder]\Images | |
| Run quality | SAV data | D:\Illumina\NextSeq Control Software Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Focus images (if requested) |
D:\Illumina\NextSeq Control Software Temp\[RunFolder]\Images | |
| Run aborted with error | SAV data | D:\Illumina\NextSeq Control Software Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Cycle logs | D:\Illumina\NextSeq Control Software Temp\[RunFolder]\Logs | |
| System check failures | System check results | D:\Illumina\SystemCheckResults\SystemCheckResultsDetails.csv Individual System Check results will be in date and time stamped folders |
| Data transfer to network (for NextSeq Control Software (NCS) v2.2 or earlier) |
RTA logs | D:\Illumina\ NextSeq Control Software Temp\[RunFolder]\Data\RTA Logs |
| Data transfer to BaseSpace Sequence Hub (for NCS v2.2 or earlier) | BaseSpace Broker logs and accessory files | D:\Illumina\basespace broker |
| Data transfer to network or BaseSpace Sequence Hub (for NCS v4 or later) |
UCS logs and accessory files | C:\ProgramData**\Illumina\UniversalCopyService\ |
*Cycle 1 failure is indicated by all cameras becoming disabled at cycle 1 due to an inability to detect clusters.
**The ProgramData folder may be hidden. To un-hide files, select the View tab in the File Explorer window and make sure Hidden Items is selected.
NextSeq 1000/2000
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Run quality | SAV data | /usr/local/illumina/runs/[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Run aborted with error | SAV data | /usr/local/illumina/runs/[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Cycle logs | /usr/local/illumina/runs/[RunFolder]/Logs | |
| Pre-run check failures | Pre-run check logs | /usr/local/illumina/runs/setup/[RunFolder] |
| Sample sheet related errors | Orchestrator logs | /usr/local/ilumina/logs/instrument-orchestrator |
| Data transfer to network or BaseSpace Sequence Hub | UCS logs and accessory files | /usr/local/illumina/logs/universal-copy-service /usr/local/illumina/persistence/universal-copy-service |
HiSeq 1000/1500/2000/2500
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Run quality | SAV data | D (FCA) or E (FCB):\Illumina\HiSeq Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Thumbnails (if requested) |
D (FCA) or E (FCB):\Illumina\HiSeq Temp\[RunFolder]\L00x\Cy.1 (Where x = lane and y = cycle number) |
|
| Run aborted with error | SAV data | D (FCA) or E (FCB):\Illumina\HiSeq Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Cycle logs | D (FCA) or E (FCB):\Illumina\HiSeq Temp\[RunFolder]\Logs | |
| Certain hardware issues | Maintenance logs | D:\Illumina Maintenance Logs
|
| Data transfer to network | RTA logs | D (FCA): or E (FCB):\Illumina\HiSeq Temp\[RunFolder]\Data\RTA Logs |
| Data transfer to BaseSpace Sequence Hub | BaseSpace Broker logs and accessory files | D:\Illumina\basespace broker |
HiSeq 3000/4000/X
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Failure to find fiducial | Auto center images | O:\Illumina\HiSeqTemp\[RunFolder]\Images |
| Run quality | SAV data | O:\Illumina\HiSeq Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Thumbnails (if requested) |
O:\Illumina\HiSeq Temp\[RunFolder]\L00x\Cy.1 (Where x = lane and y = cycle number) |
|
| Run aborted with error | SAV data | O:\Illumina\HiSeq Temp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Cycle logs | O:\Illumina\HiSeq Temp\[RunFolder]\Logs | |
| Certain hardware issues | Certain hardware issues Maintenance logs | C:\Illumina Maintenance Logs
|
NovaSeq 6000
| Type of Investigation | Logs or Files Needed | Location |
|---|---|---|
| Failure to find fiducial | Auto center images | C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder]\ Alignment |
| Run quality | SAV data | C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Run aborted with error | SAV data | C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder] InterOp Folder, RunInfo.xml, RunParameters.xml |
| Cycle logs | C:\ProgramData*\Illumina\NovaSeq\NovaSeqTemp\[RunFolder]\Logs | |
| Data transfer to network or BaseSpace Sequence Hub | UCS logs and accessory files | C:\ProgramData*\Illumina\UniversalCopyService\ |
*The ProgramData folder may be hidden. To un-hide files, select the View tab in the File Explorer window and make sure Hidden items is selected.