BaseSpace Onsite v2.1 LT System Guide - Support

BaseSpace Onsite v2.1 LT System Guide - Support
BaseSpace® Onsite v1.0 LT
System Guide
For Research Use Only. Not for use in diagnostic procedures. Revision History
Introduction
Getting Started
BaseSpace Onsite User Interface
How To Use BaseSpace Onsite
Admin Tasks
Technical Assistance
ILLUMINA PROPRIETARY
Document # 1000000002666 v00
September 2015
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Revision History
Revision History
Part #
Document #
1000000002666
v00
Date
October
2015
BaseSpace Onsite v1.0 LT System Guide
Description of Change
Initial release.
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The BaseSpace Onsite LT System is a genomics analysis platform that is a directly
integrated end-to-end solution for the MiSeq System, using MiSeq Control Software
(MCS) v2.6 or later.
BaseSpace Onsite has the following features:
} The instrument seamlessly pushes the base call (*.bcl) files and associated files to
BaseSpace Onsite for automatic analysis and storage. There is no need for a manual
and time-consuming data-transfer step.
} BaseSpace Onsite provides a mechanism to share data with others and easily scale
storage and computing needs.
} BaseSpace Onsite runs locally; no need to connect to the cloud.
Workflow Model
Processing a flow cell on a sequencing instrument produces various files, collectively
referred to as a run. A run contains log files, instrument health data, run metrics, sample
sheet, and base call information (*.bcl files). The base call information is demultiplexed
in BaseSpace Onsite to create the samples used in secondary analysis.
The result files from an app session are stored in an analysis. Analyses are created to
record every time an app is launched. For example, when a resequencing app executes
alignment and variant calling, an analysis is created that contains the app results for
each sample. App results generally contain BAM and VCF files, but they can also
contain other file types. App results can also be used as inputs to apps.
Finally, projects are simple containers that store samples and analyses.
BaseSpace Onsite v1.0 LT System Guide
7
Introduction
Introduction
Figure 1 BaseSpace Onsite Data Model
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Document # 1000000002666 v00
Introduction
BaseSpace Onsite Apps
BaseSpace Onsite supports the following apps.
App
Description
Illumina Core Apps
The following Illumina Core Apps are available:
• Isaac Whole-Genome Sequencing v4
• Isaac Enrichment v1.0
• Isaac Enrichment v2.1
• BWA Whole-Genome Sequencing v1
• BWA Enrichment v1.0
• BWA Enrichment v2.1
• TopHat Alignment v1 (multilaunch feature not available)
• Cufflinks Assembly and Differential Expression v1
• TruSeq Amplicon v1.1
• Amplicon DS v1.1
• 16S Metagenomics v1.0.1
• MethylSeq v1.0
• Small RNA v1.0
• TruSeq Targed RNA v1.0
For documentation, see the Illumina support page for BaseSpace.
VariantStudio
Illumina VariantStudio enables you to view annotation
information for variants and transcripts and filter to the variants of
interest in one easy to use application. See Run the VariantStudio
App on page 29 for instructions on launching this app, and the
BaseSpace VariantStudio User Guide for instructions on using the
software application.
Integrative
Genomics Viewer
Illumina has generated an app with the Integrative Genomics
Viewer (IGV) of the Broad Institute for visualizing your sequence
data in great detail. See Launch the IGV App on page 28 for
instructions on using this app.
BaseSpace Labs
Apps
The following apps are developed using an accelerated
development process. Illumina provides limited support for
BaseSpace Labs Apps and are provided without a warranty.
• FastQC v1.0
• FASTQ Toolkit v1.0
• Kraken Metagenomics v1.0
• Variant Calling Assessment Tool (VCAT) v.2.0
Third-Party Apps
Currently, BaseSpace Onsite provides SPAdes Genome Assembler
3.5. For more information, see the SPAdes App page on the Apps
tab.
Note—The NovoAlign app is no longer available. However, legacy
analysis results are still viewable.
BaseSpace Onsite v1.0 LT System Guide
9
App
Description
BaseMount
BaseMount is a tool that allows command line read access to your
BaseSpace Onsite data. The BaseMount app is a stand-alone
installable application that you can install on your own computer.
Then you can connect BaseMount to the data on your BaseSpace
Onsite server or servers.
For more information, see the following links:
• BaseMount Web Page
• BaseMount Help
• BaseSpace Blog
Note—BaseSpace is the default API endpoint for BaseMount. Make
sure to launch BaseMount using the correct server configuration
option for BaseSpace Onsite:
basemount --config {config_file_prefix} -api-server=http://{BSO_windows_IP}:8080
{mount-point_folder_path}
• The --config parameter is optional. Use this parameter to
mount against multiple user accounts.
• The BSO_windows_IP is the IP address that you enter in your
browser to access your BaseSpace Onsite account. The API url is
at port 8080.
• The mount-point_folder_path is the path to a user-created
directory on the system where BaseMount is running.
Annotation Options
Depending on the application used, the following annotation options are available.
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Option
Description
Illumina
Annotation
Service
RefSeq or Ensembl
This option utilizes the Illumina Annotation Service (hosted at
annotation.basespace.illumina.com) to provide annotation of
variants (SNPs, insertions, and deletions) in the sample VCF files.
This service requires an external network connection and also
requires you to whitelist the IP address of your BaseSpace Onsite
system.
Basic
Annotation with
local genome files
from the UCSC
hg19 genome
This option utilizes a basic set of annotations, including SNPs and
indels, using the genome files hosted locally on the BaseSpace
Onsite system. This option does not require an external network
connection.
On-node analysis
RefSeq or Ensembl
This option is a localized version of Illumina Annotation Service
provided with the BaseSpace Onsite v2.1 software update. It
provides annotations for known variants as provided by Illumina
Annotation Service, and can also predict novel variants. This option
does not require an external network connection.
None
No annotation is performed with this option. The reports
generated for analyses using this option shows either a 0 or N/A
for the various annotations.
Document # 1000000002666 v00
The following apps provide the Illumina Annotation Service, Basic, or None options:
} BWA Enrichment v1.0
} BWA Whole Genome Sequencing v1.0
} Isaac Enrichment v1.0
} Isaac Whole Genome Sequencing v2
The Isaac Whole Genome Sequencing v4.0 application can perform annotation on-node,
without the need for an external network connection to the Illumina Annotation Service.
All other applications on BaseSpace Onsite do not provide annotation options. To
perform annotation on the results of these analyses, you can use the VariantStudio
application, which also performs annotation using the Illumina Annotation Service.
BaseSpace Onsite v1.0 LT System Guide
11
Introduction
The following apps provide either the Illumina Annotation Service or None options:
} Amplicon DS v1.0
} BWA Enrichment v2.1
} Isaac Enrichment v2.1
} TruSeq Amplicon v1.1
Getting Started
Make sure to have a compatible desktop computer. BaseSpace Onsite is compatible with
Internet Explorer (10 or higher), Chrome (43 or higher), Firefox (38 or higher), and Safari
(8 or higher). Hardware requirements for these browsers can be found on the developer
website. A PC running Windows 7 or greater is required to access the BaseSpace Onsite.
NOTE
When connecting your instrument to BaseSpace Onsite, you are asked to enter the full
path to your BaseSpace Onsite server. Your BaseSpace Onsite IP address can be found in
the broker configuration file of the sequencing system that you want to connect BaseSpace
Onsite to. The BaseSpace Onsite IP address is included as part of the API URL value.
Using BaseSpace Onsite with MiSeq
The MiSeq System features an option to send instrument health and sequencing data to
BaseSpace Onsite in real time to streamline both instrument quality control and analysis.
Real-time monitoring of runs enables fast troubleshooting. Free alignment and variant
calling provide many easy to use workflows that tailor analysis for diverse biological
applications.
When you set up the run on the MiSeq, select the option to log in to BaseSpace Onsite.
For more information, see MiSeq Connection on page 12.
NOTE
Raw data from the run is also stored on the instrument, or in the location of the output
folder that you specified in the Storage screen.
BaseSpace Onsite automatically disconnects from the MiSeq at the end of the run or
when all RTA analysis files have finished uploading. If the internet connection is
interrupted, analysis files continue uploading after the connection is restored from the
point when the interruption occurred.
When the last base call file is uploaded to BaseSpace Onsite, secondary analysis of your
data begins. For information about how to run tasks, see How To Use BaseSpace Onsite on
page 21.
NOTE
Unlike BaseSpace, BaseSpace Onsite does not have a MiSeq Reporter app. BaseSpace
Onsite directs all workflow types uploaded from MiSeq through the GenerateFASTQ app.
To perform additional secondary analysis, manually launch the relevant app or apps on
the resulting FASTQ samples.
MiSeq Connection
Perform the following steps to connect MiSeq to BaseSpace Onsite.
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1
Make sure that you have MCS version 2.6 or later. If you do not, upgrade your MCS.
2
Make sure that you have a stable internet connection of at least 10 Mbps upload
speed from the MiSeq.
3
During run configuration, enter the full path to your BaseSpace Onsite server.
Document # 1000000002666 v00
Select or clear When using BaseSpace or BaseSpace Onsite, replicate analysis
locally on MiSeq.
The Replicate Analysis Locally setting specifies analysis processing locations when
using BaseSpace Onsite. The setting provides the option to perform analysis both
locally on the instrument and in BaseSpace Onsite. Consider the following items
when selecting or deselecting this option:
} If you select this option, MiSeq Reporter launches automatically after the run and
performs analysis locally.
} If you do not select this option, MiSeq Reporter does not launch automatically after
the run and analysis is performed in BaseSpace Onsite only.
} If performing the VeriSeq PGS workflow with BlueFuse Multi, select this option.
5
Click Save and Return.
6
When starting a sequencing run, select Use BaseSpace Onsite for storage and
analysis on the BaseSpace Options screen.
NOTE
To use BaseSpace Onsite, load a sample sheet at the start of your run.
For more information, see the MiSeq System Guide (document # 15027617).
When you begin your sequencing run on the MiSeq, the BaseSpace Onsite icon changes
to indicate that the MiSeq is connected to BaseSpace Onsite and data files are being
transferred.
Getting Shared Data
If you receive a link to shared data in BaseSpace Onsite, click the link.
If someone shares data with you, you receive a notification. The shared data show up in
your project list. Now you can use the BaseSpace Onsite tools to look at and download
the data. For information about how to run tasks, see How To Use BaseSpace Onsite on
page 21.
NOTE
The owner of the data can disable the sharing feature at any time.
BaseSpace Onsite v1.0 LT System Guide
13
Getting Started
4
BaseSpace Onsite User Interface
This section describes the various aspects of the BaseSpace Onsite UI.
} Toolbar on page 14
} MyAccount on page 14
} Admin Panel on page 15
} Dashboard Tab on page 15
} Prep Tab on page 16
} Runs Tab on page 17
} Projects Tab on page 18
} Apps Tab on page 20
Toolbar
The BaseSpace Onsite toolbar elements are listed in the following table.
Icon
Element
Description
Dashboard See Dashboard Tab on page 15.
Tab
Prep Tab
See Prep Tab on page 1.
Runs Tab
See Runs Tab on page 17.
Projects
Tab
See Projects Tab on page 18.
Apps Tab
See Apps Tab on page 20.
Support
Page
The BaseSpace Onsite Support page provides access to the
BaseSpace Onsite Knowledge Base, User Guide, and Illumina
Technical Support.
The Search box allows you to find runs, projects, samples, files,
or apps. For more information, see Search for Runs, Projects,
Samples, Files, and Apps on page 50.
The Account drop-down list provides access to:
• MyAccount—See MyAccount on page 14
• Trash—See Delete Items on page 47
• Terms—Leads to the User Agreement
• Blog—Leads to the blog, which includes latest news,
developments, and updates
• Sign out
Search
Account
MyAccount
Settings
On the Settings page you can edit your notifications settings, edit your profile, or update
your profile picture.
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Document # 1000000002666 v00
The Transfer History page allows you to review projects or runs that have been
transferred. For more information, see Transfer Owner on page 46.
Library Prep Kits
The Library Prep Kits page shows all the available library prep kits in Sample Prep. To
enter a custom kit, click New. Custom kits allow you to define nonstandard index
combinations and to define your own default layout for the indexes on a plate.
Storage
The Storage page shows the total amount of storage used (owned by you and shared)
and the amount of storage used in Runs, Projects, and Trash.
Admin Panel
The Admin Panel allows you to manage analysis, notifications, storage, users, system
health, planned runs, software updates, and alarms. See Admin Tasks on page 51 for a
description.
NOTE
You need administrator privileges to see and work in the admin panel.
Dashboard Tab
After login, the first tab you see is the dashboard. The dashboard provides access to
storage information, the developers page, the newsfeed, notifications, latest runs, and
latest analyses. The dashboard is always accessible in BaseSpace Onsite from the top
ribbon selector.
NOTE
If a run or project is not showing on BaseSpace Onsite, it is possible your data has not been
sent to BaseSpace Onsite. Set the BaseSpace Onsite option on your sequencing instrument.
For more information, see the system guide for your instrument.
Storage
The storage pane shows the total amount of storage used (used by you and shared). Click
the Details button to open the Storage page under My Account.
Developers
Click the Details button on the Developers pane to go to the BaseSpace developer portal.
Access to the BaseSpace developer portal requires an external internet connection outside
of your local network.
Newsfeed
The Newsfeed pane shows the most recent posts from the BaseSpace blog. Click an
article name to open the article, or click the Read more link at the bottom of the pane to
open the BaseSpace blog.
The Newsfeed pane requires an external internet connection outside of your local
network to show content. Access to the BaseSpace blog also requires an external internet
connection.
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BaseSpace Onsite User Interface
Transfer History
Notifications
This pane shows invitations to shared projects, along with other notifications and alerts.
The most recent notifications listed first. There are multiple types of notifications:
} Runs
} Run in progress
} Run completed
} Run error
} Collaborators
} Collaborator joined a project/run of which you are a member
} Collaborator invited you to a project/run
} (optionally) collaborator has included a personal message
} Collaborator recommended an App
} Collaborator accepted your offer to transfer ownership
} Collaborator offered to transfer ownership to you.
} Analyses by you
} Analysis in progress
} Analysis completed
} Analysis error
} Analyses by collaborators
} Analysis in progress
} Analysis completed
} Analysis error
} Uploads, additions, or deletions to/from a project of which you are a member
} By you
} By a collaborator
NOTE
If you did not configure SMTP during install, all notifications show up on the dashboard.
No notifications are sent through email.
Latest Runs
The Latest Runs pane shows the 3 most recent runs with their dates and status, and is
updated automatically.
Click All Runs to open the Runs tab. Clicking a run opens the Runs tab with the run
loaded. For more information, see Runs Tab on page 17.
Latest Analyses
The Latest Analyses pane shows the 3 most recent analysis with their dates and status,
and is updated automatically.
Click All Analyses to open the Analyses page, which lists all analysis results, along with
the application used, project name, date updated, size of the result, and status.
Clicking an analysis on the dashboard pane opens the specific analysis report. For more
information, see Analyses Page on page 19.
Prep Tab
The Prep tab is not supported on the BaseSpace Onsite LT System.
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The Runs button leads to the runs list, which allows you to sort your runs based on
experiment name, state, workflow, created date, machine, and owner.
The following run states are possible. The blue boxes indicate final states.
If you want to look at a run in detail, click the name to view metrics in more detail. For
more information, see Run Overview Page on page 17.
You manage the runs by using the buttons above the list:
} Share—Manage sharing a run with a particular collaborator. See Share a Run Using
the Email Option on page 43.
} Get Link—Forward the sharing link to any number of collaborators. See Share a Run
with Get Link on page 43.
} Download Run—Download files from this run. See Download Run File Package on
page 31.
} Transfer Owner—Hand control of data over to a collaborator or customer. This
button is visible if a run is selected. See Transfer Owner on page 46.
} Move to Trash—Delete a project. This button is visible if a run is selected. See Delete
Project on page 47.
} View Trash—View the deleted items in the trash, so you can restore the items or
empty the trash. See Delete Items on page 47.
NOTE
Runs and projects have separate permissions. If you share a project, you do not share the
runs contained within the project.
Run Overview Page
The Run Overview page provides 5 panes:
} Run Details—Provides a summary of the run with links to view files and download
and share options. For more information, see Share Data on page 41, View Files and
Results on page 21, or Download Files on page 30.
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BaseSpace Onsite User Interface
Runs Tab
}
}
}
}
Samples —Provides a list of all the app results in the run, the associated projects,
and the number of samples in that analysis.
Charts—Shows an intensity by cycle chart. Clicking the header takes you to the
Charts page, which contains 5 charts with run metrics.
Run Summary—Shows tables with basic data quality metrics. Clicking the header
takes you to the Run Summary page.
Indexing QC—Lists count information for indexes used in the run. Clicking the
header takes you to the Indexing QC page.
In addition, the Side Navigation ribbon provides easy navigation in the Run Details
area.
Run Samples List
The samples list allows you to sort the samples in your run based on sample ID, app,
date created, and project. If you want to look at a sample, app result, or project in detail,
click the links to get to the following pages:
} Sample Overview Page on page 19.
} Analyses Page on page 19.
} Project Overview Page on page 18.
In addition, the Side Navigation ribbon provides easy navigation in the Run Details
area.
Projects Tab
The Projects button opens a list of your projects. You can sort the list by name, last
update, or owner. Clicking a project provides access to the app results and samples
within that project.
You manage the projects by using the buttons above the list:
} New Project—Generate a new project. See Set Up a New Project on page 44.
} Edit project—Edit the name and description of the project. See Edit Project Details on
page 44.
} Share Project—Manage sharing a project with a particular collaborator. See Share a
Project Using the Email Option on page 42.
} Get Link—Forward the sharing link to any number of collaborators. See Share a
Project using the Get Link option on page 42.
} Transfer Owner—Hand control of data over to a collaborator or customer. See
Transfer Owner on page 46.
} Move to Trash—Delete a project. This button is visible if a project is selected. See
Delete Project on page 47.
} View Trash—View the deleted items in the trash, so you can restore them or empty
the trash. See Delete Items on page 47.
NOTE
Runs and projects have separate permissions. If you share a project, you do not share the
runs contained within the project.
Project Overview Page
The Project Overview page provides access to 3 panes with information about the
project:
} About—Provides summary information about the project, including the project
owner, shared status, date created, and collaborators.
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}
Analyses—Provides a list of all the App Sessions in the project. This tab can be
sorted based on analysis name, last modified date created, status, or application
used to generate the analysis. Clicking the analysis links to the app results for that
sample. For more information, see Analyses Page on page 19.
Samples—Provides a list of all the samples in the project. Clicking a sample links to
the page for that sample. For more information, see Sample Overview Page on page 19.
Selecting the samples allows you to launch it in an app, copy to a different project, or
combine with another result.
NOTE
You can access these panes through the left navigation bar.
Project Toolbar
The Project toolbar provides the following actions:
} Launch app—Run apps on your sample. Clicking the app name leads to a page with
more information about launching that app, including access permissions. See
Analyze Samples Further on page 28.
} Download Project—Download all files in a project. See Download Project or Analysis
Package on page 1.
} Import—Upload files to a project. See Upload Files on page 45.
} Share project—Manage sharing a project with a particular collaborator. See Share a
Project Using the Email Option on page 42.
} Get link—Forward the sharing link to any number of collaborators. See Share a
Project using the Get Link option on page 42.
} Edit project—Edit the name and description of the project. See Edit Project Details on
page 44.
} Transfer Owner—Hand control of data over to a collaborator or customer. See
Transfer Owner on page 46.
} Move to Trash—Move the project to the trash. Deleting a project deletes all
associated data, including samples and analyses. See Delete Project on page 47.
} View Trash—View all deleted runs, projects, analyses, and samples. See Delete Items
on page 47.
Options that are not available for the particular analysis or sample are grayed out.
If you have selected samples in the Samples pane, you can perform additional actions:
} Copy to...—Copy samples from this project to another. See Copy Samples on page 45.
} Combine—Combine samples. See Combine Samples on page 44.
The app session states are defined as follows.
State
Running
Complete
Aborted
Needs
Attention
Description
The app is processing or uploading data.
Processing and file upload has finished and the data are now available to
use.
This AppResult or Sample has been aborted and cannot be resumed.
Cannot continue without user intervention.
Analyses Page
Sample Overview Page
The Sample Overview page provides 2 panes:
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BaseSpace Onsite User Interface
}
}
}
Sample Details—Provides a summary of the run with a links to launch a custom
BaseSpace Onsite app on your sample. Clicking the app name leads to a page with
more information about that app, including access permissions.
Running apps can incur a charge.
Files—Provides a list of files associated with that sample. You can either look at all
FASTQ files, or look at files specific for an app session.
For more information, see View Files and Results on page 21. You can also download
selected files; see Download Multiple FASTQ Files on page 30.
Apps Tab
The Apps button leads to the Apps page, which provides an overview of the custom
BaseSpace Onsite apps that you can run.
} Clicking the app name leads to a page with more information about that app,
including the version, a link to the developer, and their app support contact details.
} Clicking the Launch button leads you through the launch pages, which allow you to
set up the app session. Specify parameters like the project, sample, or output folder
used by the app, depending on the app, and accept access permissions.
} You can search for apps using Search.
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How To Use BaseSpace Onsite
How To Use BaseSpace Onsite
The following topics describe how to run different functions in BaseSpace Onsite.
} View Files and Results on page 21
} Download Files on page 30
} Project and Sample Management on page 44
} Search for Runs, Projects, Samples, Files, and Apps on page 50
View Files and Results
The following topics describe how to view files and results in BaseSpace Onsite.
View Files from a Run
BaseSpace Onsite gives you an option to view your run files or download them
individually.
To view files, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
3
From the Run Overview Page, select the Files icon
4
Select the desired file to view.
from the left navigation menu.
See BaseSpace Onsite Files on page 31 for a description of the available files.
View Indexing QC Page
The Indexing QC page lists count information for indexes used in the run. The Indexing
QC is only available if the run is an index run.
By viewing the indexing QC results, you can see unexpected results for a sample with a
particular index and use the information for troubleshooting purposes. You can also use
this feature to confirm that all indexed samples were represented properly.
To view indexing QC results, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
3
There are 2 methods to go to the Indexing QC page:
} From the Run Overview page, click the Indexing QC link.
} From the Run Overview page, click the Indexing QC icon
navigation menu.
from the left
You can select the displayed lane through the drop-down list.
The first table provides an overall summary of the indexing performance for that lane,
including the following information.
Total Reads
The total number of reads for this lane.
PF Reads
The total number of passing filter reads for this lane.
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% Reads Identified
(PF)
The total fraction of passing filter reads assigned to an index.
CV
The coefficient of variation for the number of counts across all
indexes.
Min
The lowest representation for any index.
Max
The highest representation for any index.
Further information is provided regarding the frequency of individual indexes in both
table and graph form. The table includes the following columns.
Index Number
A unique number assigned to each index by BaseSpace Onsite for
display purposes.
Sample ID
The sample ID assigned to an index in the sample sheet.
Project
The project assigned to an index in the sample sheet.
Index 1 (I7)
The sequence for the first Index Read.
Index 2 (I5)
The sequence for the second Index Read.
% Reads Identified
(PF)
The number of reads (only includes Passing Filter reads) mapped
to this index.
This information is also displayed in graphical form. In the graphical display, indexes
are ordered according to the unique Index Number assigned by BaseSpace Onsite.
View Run Charts
The Charts page shows charts with run metrics.
1
Click the Runs icon.
2
Click the desired run.
3
There are 2 methods to go to the Charts page:
} From the Run Overview page, click the Charts link.
} From the Run Overview page, click the Charts icon
menu.
from the left navigation
Flow Cell Chart
The Flow Cell chart shows color-coded graphical quality metrics per tile for the entire
flow cell.
Use the Flow Cell chart to judge local differences per cycle, per lane, or per read in
sequencing metrics on a flow cell. It is also an easy way to see the %Q30 metric, which is
an excellent single metric to judge a run. Do not use the Flow Cell chart to look at
downstream analysis metrics.
The Flow Cell chart has the following features:
} You can select the displayed metric, surface, cycle, and base through the drop-down
lists.
} The color bar to the right of the chart indicates the values that the colors represent.
} The chart is displayed with tailored scaling by default.
} Tiles that have not been measured or are not monitored are gray.
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Intensity
This chart shows the intensity by color and cycle of the 90%
percentile of the data for each tile.
FWHM
The average full width of clusters at half maximum (in pixels). Used
to display focus quality.
% Base
The percentage of clusters for which the selected base (A, C, T, or
G) has been called.
%Q > 20, %Q > 30
The percentage of bases with a quality score of > 20 or > 30,
respectively. These charts are generated after the 25th cycle, and
the values represent the current scored cycle.
Median Q-Score
The median Q-Score for each tile over all bases for the current
cycle. These charts are generated after the 25th cycle. This plot is
best used to examine the Q-scores of your run as it progresses.
Bear in mind that the %Q30 plot can give an over simplified view
due to its reliance on a single threshold.
Density
The density of clusters for each tile (in thousands per mm 2 ).
Density PF
The density of clusters passing filter for each tile (in thousands per
mm 2 ).
Clusters
The number of clusters for each tile (in millions).
Clusters PF
The number of clusters passing filter for each tile (in millions).
Error Rate
The calculated error rate, as determined by a spiked in PhiX control
sample. If no PhiX control sample is run in the lane, this chart is not
available.
% Phasing, %
Prephasing.
The estimated percentage of molecules in a cluster for which
sequencing falls behind (phasing) or jumps ahead (prephasing) the
current cycle within a read.
% Aligned
The percentage of reads from clusters in each tile that aligned to
the PhiX genome.
Perfect Reads
The percentage of reads that align perfectly, as determined by a
spiked in PhiX control sample. If no PhiX control sample is run in
the lane, this chart is all gray.
Corrected Intensity
The intensity corrected for cross talk between the color channels
by the matrix estimation and phasing and prephasing.
Called Intensity
The intensity for the called base.
Signal to Noise
The signal to noise ratio is calculated as mean called intensity
divided by standard deviation of noncalled intensities.
Note the variable scales used on these different parameters.
Data By Cycle Plot
The Data by Cycle plot shows the progression of quality metrics during a run as a line
graph.
Use the Data By Cycle plot to judge the progression of quality metrics during a run on a
cycle by cycle basis. Do not use the Data By Cycle plot to look at downstream analysis
metrics, or aggregate analysis for a whole lane regardless of cycle.
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How To Use BaseSpace Onsite
You can monitor the following quality metrics using the Flow Cell chart.
The Data by Cycle plots have the following features:
} You can select the displayed metric and base through the drop-down lists.
} The symbol in the top right-hand corner toggles the plot between pane view and full
screen view.
You can monitor the following quality metrics with this plot.
Intensity
This chart shows the intensity by color and cycle of the 90%
percentile of the data for each tile.
FWHM
The average full width of clusters at half maximum (in pixels). Used
to display focus quality.
% Base
The percentage of clusters for which the selected base (A, C, T, or
G) has been called.
%Q > 20, %Q > 30
The percentage of bases with a quality score of > 20 or > 30,
respectively. These charts are generated after the 25th cycle, and
the values represent the current scored cycle.
Median Q-Score
The median Q-Score for each tile over all bases for the current
cycle. These charts are generated after the 25th cycle. This plot is
best used to examine the Q-scores of your run as it progresses.
Bear in mind that the %Q30 plot can give an over simplified view
due to its reliance on a single threshold.
Error Rate
The calculated error rate, as determined by a spiked in PhiX control
sample. If no PhiX control sample is run in the lane, this chart is not
available.
Perfect Reads
The percentage of reads that align perfectly, as determined by a
spiked in PhiX control sample. If no PhiX control sample is run in
the lane, this chart is all gray.
Corrected Intensity
The intensity corrected for cross talk between the color channels
by the matrix estimation and phasing and prephasing.
Called Intensity
The intensity for the called base.
Signal to Noise
The signal to noise ratio is calculated as mean called intensity
divided by standard deviation of noncalled intensities.
You can expand a chart by clicking the expand button
.
Q-score Distribution
The Q-score Distribution plot shows a bar graph that allows you to view the number of
bases by quality score. The quality score is cumulative for current cycle and previous
cycles, and only bases from reads that pass the quality filter are included.
Use it to judge the Q-score distribution for a run, which is an excellent indicator for run
performance. Do not use the Q-score Distribution plot to look at metrics other than
quality scores.
The Q-score Distribution pane shows plots that allow you to view the number of reads
by quality score. The quality score is cumulative for current cycle and previous cycles,
and only reads that pass the quality filter are included.
These plots have the following features:
} You can select the displayed read, and cycle through the drop-down lists.
} The symbol in the top right-hand corner toggles the plot between pane view and full
screen view.
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You can slide the threshold (set at ≥ Q30 by default) to examine the proportion of bases
at or above any particular Q-score. When using Q-score binning, this plot reflects the
subset of Q-scores used.
Data by Lane Plot
The Data by Lane plots allow you to view quality metrics per lane.
Use the Data By Lane plot to judge the difference in quality metrics between lanes. Do
not use the Data By Lane plot to look at alignment or variant calling analysis metrics.
The Data by Lane plots have the following features:
} You can select the displayed metric through the drop-down lists.
} The symbol in the top right-hand corner toggles the plot between pane view and full
screen view.
The plots share several characteristics:
} The plots show the distribution of mean values for a given parameter across all tiles
in a given lane.
} The red line indicates the median tile value for the parameter displayed.
} Blue boxes are for raw clusters, green boxes for clusters passing filter.
} The box outlines the interquartile range (the middle 50% of the data) for the tiles
analyzed for the data point.
} The error bars delineate the minimum and maximum without outliers.
} The outliers are the values that are more than 1.5 times the interquartile range below
the 25th percentile, or more than 1.5 times the interquartile range above the 75th
percentile. Outliers are indicated as dots.
You can monitor the following quality metrics with this plot:
} The density of clusters for each tile (in thousands per mm2).
} The number of clusters for each tile (in millions).
} The estimated percentage of molecules in a cluster for which sequencing falls behind
(phasing) or jumps ahead (prephasing) the current cycle within a read.
} The percentage of reads from clusters in each tile that aligned to the PhiX genome.
You can expand a chart by clicking the expand button
.
Q-score Heat Map
The Q-score heat map shows plots that allow you to view the Q-score by cycle.
View the Q-score heat map for a quick overview of the Q-scores over the cycles. Do not
use the Q-score heat map to look at metrics other than quality scores.
These plots have the following features:
} The color bars to the right of each chart indicate the values that the colors represent.
The charts are displayed with tailored scaling; the scale is always 0% to 100% of
maximum value.
} The symbol in the top right-hand corner toggles the plot between pane view and full
screen view.
You can expand a chart by clicking the expand button
BaseSpace Onsite v1.0 LT System Guide
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How To Use BaseSpace Onsite
The Q-score is based on the Phred scale. The following list shows Q-scores and the
corresponding chance that the base call is wrong:
} Q10—10% chance of wrong base call
} Q20—1% chance of wrong base call
} Q30—0.1% chance of wrong base call
} Q40—0.01% chance of wrong base call
View Run Samples List
The Run Samples List contains a list of all the samples in the run.
Use this option when you want to see a list of all the samples in the run or to navigate to
details regarding a specific sample.
To view the Run Samples List, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
3
There are 2 methods to go to the Run Samples List:
} From the Runs Overview page, click the Samples link.
} From the Runs Overview page, click the Samples icon
menu.
from the left navigation
You can now click a sample to see the sample overview; for more information, see
Sample Overview Page on page 19.
View Run Summary
The Run Summary page has the overall statistics about the run.
Use this option when you want to view information about the run such as percent
alignment, cycles, and densities.
To view the Run Summary page, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
3
There are 2 methods to go to the Run Summary:
} From the Run Overview Page, select Run Summary button.
} From the Run Overview Page, select the Run Summary icon
navigation menu.
from the left
The following metrics are displayed in the top table, split out by read and total.
Level
The sequencing read level.
Yield Total
The number of bases sequenced, which is updated as the run
progresses.
Projected Total
Yield
The projected number of bases expected to be sequenced at the
end of the run.
Aligned
The percentage of the sample that aligned to the PhiX genome,
which is determined for each level or read independently.
Error Rate
The calculated error rate of the reads that aligned to PhiX.
Intensity Cycle 1
The average of the A channel intensity measured at the first cycle
averaged over filtered clusters. For the NextSeq 500 System, the
red channel is used.
%Q ≥ 30
The percentage of bases with a quality score of 30 or higher,
respectively. This chart is generated after the 25th cycle, and the
values represent the current cycle.
The following metrics are available in the Read tables, split out by lane.
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The number of tiles per lane.
Density
The density of clusters (in thousands per mm 2 ) detected by
image analysis, +/- 1 standard deviation.
Clusters PF
The percentage of clusters passing filtering, +/- 1 standard
deviation.
Phas./Prephas.
The value used by RTA for the percentage of molecules in a cluster
for which sequencing falls behind (phasing) or jumps ahead
(prephasing) the current cycle within a read.
For MiSeq and NextSeq, RTA generates phasing and prephasing
estimates empirically for every cycle. The value displayed here is
therefore not used in the actual phasing/prephasing calculations,
but is an aggregate value determined from the first 25 cycles. For
most applications, the value reported is very close to the value that
is applied. For low diversity samples or samples with unbalanced
base composition, the reported value can diverge from the values
being applied because the value changes from cycle to cycle.
Reads
The number of clusters (in millions).
Reads PF
The number of clusters (in millions) passing filtering.
%Q ≥ 30
The percentage of bases with a quality score of 30 or higher,
respectively. This chart is generated after the 25th cycle, and the
values represent the current cycle.
Yield
The number of bases sequenced which passed filter.
Cycles Err Rated
The number of cycles that have been error-rated using PhiX,
starting at cycle 1.
Aligned
The percentage that aligned to the PhiX genome.
Error Rate
The calculated error rate, as determined by the PhiX alignment.
Subsequent columns display the error rate for cycles 1–35, 1–75,
and 1–100.
Intensity Cycle 1
The average of the A channel intensity measured at the first cycle
averaged over filtered clusters.
View the Project Sample List
The Project Sample List contains the list of samples in a project. Use this option when
you want to see a list of all the samples in the project or navigate to details regarding a
specific sample.
To view the Project Sample List, perform the following steps.
1
Click the Projects icon.
2
Click the desired project.
3
Click the Samples link from the left navigation menu.
You can now click a sample to see the sample overview; for more information, see
Sample Overview Page on page 19.
View the Analyses List
The Analyses List contains a list of app sessions in a project. Use this option when you
want to navigate to details regarding a specific app session.
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How To Use BaseSpace Onsite
Tiles
To view the Analyses List, perform the following steps.
1
Click the Projects icon.
2
Click the desired project.
You can now click an Analysis to see the results; for more information, see Analyses Page
on page 19.
Analyze Samples Further
The following topics describe how to analyze samples further in BaseSpace Onsite.
} Launch Apps on page 28
} Launch the IGV App on page 28
} Run the VariantStudio App on page 29
Launch Apps
You can launch apps that perform additional analysis, visualization, or annotation of
data.
To launch an app, perform the following steps.
1
There are 2 ways to start an app:
} Navigate to the project, sample, or analysis that you want to run the app on, click
the Launch Apps button, and select the desired app from the drop-down list.
} Go to the Apps button, select the desired app from the list and click Launch. If you
are running BWA Enrichment v2.1 or Isaac Enrichment v2.1, read Enrichment v2.1
Apps Adapter Trimming on page 30.
2
Read the End-User License Agreement and permissions, and then click Accept.
The app now guides you through the start-up process. BaseSpace Onsite has limited
storage capacity, and checks the free space available before starting an app. If there is not
enough available space, BaseSpace Onsite displays an error message. For more
information, see Storage Check on page 53.
Launch the IGV App
The Integrative Genomics Viewer (IGV) of the Broad Institute is a fully featured genome
browser that allows you to visualize your sequence data in great detail. Illumina has
modified IGV to display alignment and variant data from BaseSpace Onsite (BAM and
VCF files).
IGV enables you to perform variant analysis after launching Resequencing or Amplicon
workflows in BaseSpace Onsite. IGV is run on a project, which is the highest level
directory and contains one or more AppResults. IGV retains all its native functions,
including loading data from your local computer.
NOTE
Make sure that the Java Runtime Environment is installed on the computer in order for
IGV to work properly. Download Java here: java.com/en/.
Perform the following steps to launch the IGV app.
28
1
Click the Projects icon.
2
Click desired project.
3
Click the Launch Apps button and select the IGV application from the drop-down
list.
Document # 1000000002666 v00
Select the Accept button.
5
Depending on your browser, it asks you to open or save the *.jnlp file.
} For Internet Explorer, click the Open button.
} For Chrome, click the Keep button and then click file to open.
} For Firefox, select the Open with Java(TM) Web Start Launcher (default) option.
The IGV App opens on your desktop with the requested project loaded.
BaseSpace Onsite Data in IGV
The BaseSpace Onsite file browser shows data in BaseSpace Onsite that is available for
viewing in IGV. The directory structure shown is according to how data are organized in
BaseSpace Onsite.
A project is the highest level directory and it contains one or more AppResults. If an
AppResult was the result of analyzing a single sample, then the sample name is
appended to the AppResult name. Each AppResult contains zero or more files.
The file browser shows alignment (BAM) and variant (VCF) files, and, if produced, BED,
GTF, and BEDGRAPH files. Double-click a file to load it as an IGV track. First load VCF
files before BAM files because read tracks can take up an entire IGV screen, which
requires scrolling to see variants.
Additional Reference Genomes
IGV contains several installed reference genomes:
} Homo sapiens: Human hg19
} Mus musculus: Mouse mm9
} Saccharomyces cerevisiae: S. cerevisiae (sacCer2)
} Arabidopsis thaliana: A. thaliana (TAIR10)
Run the VariantStudio App
The Illumina VariantStudio data analysis software application enables researchers to
identify and classify disease-relevant variants quickly, and then communicate significant
findings in concise and actionable reports.
This application provides an intuitive framework for nonexpert users and offers the
following features:
} Flexible filtering options
} Streamlined variant classification
} Rapid and rich annotations
} Customizable reporting
Use VariantStudio if you want to perform the following:
} Explore and isolate key variants
} Categorize variants and determine biological impact
To launch the VariantStudio app, perform the following steps.
1
Click the Apps button.
2
Select the VariantStudio app from the list and click Launch.
3
Select the project you want to run the app on. You can only select projects you own.
4
Click Continue.
5
If you use the app for the first time, install VariantStudio:
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4
a
b
c
6
Click the Install VariantStudio button.
Run the setup.exe file. Your web browser can ask you to save the file first. After
the download has completed, double-click the setup file.
If you are prompted with a security warning, click Install.
Click the Launch VariantStudio.
The VariantStudio application opens on your desktop with the requested project
loaded. For instructions on how to run VariantStudio, see the VariantStudio User
Guide.
Enrichment v2.1 Apps Adapter Trimming
BWA Enrichment v2.1 and Isaac Enrichment v2.1 Apps do not support adapter
trimming in this BaseSpace Onsite release. Here are some notes on the use of these apps:
} NextSeq—You do not need to use adapter trimming for NextSeq data in any of the
secondary analysis apps. Adapter trimming is performed automatically in FASTQ
generation based on the library prep kit type selected during run setup in the Prep
Tab workflow.
} HiSeq—You can go back to the uploaded run and requeue FASTQ generation by
fixing the sample sheet. To fix the sample sheet, add the adapter sequences to the
Settings subsection, and then requeue the analysis. For more information, see Fix
Sample Sheet / Rerun Workflow on page 49.
} MiSeq—You can only upload MiSeq FASTQ files through BaseSpace Onsite Import.
Trim the adapters from the FASTQ files before import.
Download Files
The following topics describe how to download files in BaseSpace Onsite.
} Download Individual Files on page 30
} Download Multiple FASTQ Files on page 30
} Download Run File Package on page 31
} Download Project or Analysis Package on page 1
Download Individual Files
BaseSpace Onsite allows you to download data as a package, individually, or as a group
of FASTQ files. Use this option when you want to download individual files, and do not
need all files for a run, sample, project, or analysis.
To download multiple FASTQ files, perform the following steps.
1
Click the Runs icon or Projects icon.
2
Navigate to the file you want to download
3
Click the file.
4
Click the Download button.
BaseSpace Onsite now downloads the files to the desired location.
Download Multiple FASTQ Files
BaseSpace Onsite allows you to download data as a package, individually, or as a group
of FASTQ files. If you want to download FASTQ files per sample, use this option to save
time.
To download multiple FASTQ files, perform the following steps.
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Click the Runs icon or Projects icon.
2
Click the desired run or project.
3
Click the desired sample in the Samples pane.
4
In the Files pane, select the checkboxes for the desired FASTQ files.
5
Click the Download Selected button.
The BaseSpace Onsite Downloader guides you through the download process, and
starts the download of the files to the desired location.
Download Run File Package
BaseSpace Onsite allows you to download data as a package, individually, or as a group
of FASTQ files. This topic describes how to download a package of files in a run.
The packages available depend on your workflow; packages that are grayed out are not
available for download. There are 4 types of data packages:
} Variant Data, containing VCF files with variant calls.
} Aligned Data, containing BAM files with aligned reads.
} Unaligned Data, containing FASTQ files with unaligned reads.
} SAV Data, containing files describing the set-up of the run and InterOp files.
For more information about file types, see BaseSpace Onsite Files on page 31.
To download a run file package, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
BaseSpace Onsite Files
BaseSpace Onsite uses and produces various files. See the topics in this section for
details.
} BAM Files on page 31
} gVCF Files on page 32
} VCF Files on page 36
} FASTQ Files on page 38
} Health Runs on page 41
BAM Files
What is it?
The Sequence Alignment/Map (SAM) format is a generic alignment format for storing
read alignments against reference sequences, supporting short and long reads (up to 128
Mb) produced by different sequencing platforms. SAM is a text format file that is humanreadable. The Binary Alignment/Map (BAM) keeps the same information as SAM, but in
a compressed, binary format that is only machine readable.
When to use it
Allows you to see alignments. Use it for direct interpretation or as a starting point for
further analysis with downstream analysis tools that are compatible with BAM. BAM
files are suitable for viewing with an external viewer such as IGV or the UCSC Genome
Browser.
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1
When not to use it
Do not use it with tools that are not compatible with the BAM format. Do not use with
applications that cannot handle large files, as BAM files can get large, depending on the
application and data.
How to use it
If you use an app in BaseSpace that uses BAM files as input, the app locates the file
when launched. If using BAM files in other tools, download the file to use it in the
external tool.
Detailed Description
Go to samtools.sourceforge.net/SAM1.pdf to see the exact SAM specification.
gVCF Files
What is it?
This application also produces the Genome Variant Call Format file (gVCF). gVCF was
developed to store sequencing information for both variant and nonvariant positions,
which is required for human clinical applications. gVCF is a set of conventions applied
to the standard variant call format (VCF) 4.1 as documented by the 1000 Genomes
Project. These conventions allow representation of genotype, annotation, and other
information across all sites in the genome in a compact format. Typical human wholegenome sequencing results expressed in gVCF with annotation are less than 1 Gbyte, or
about 1/100 the size of the BAM file used for variant calling. If you are performing
targeted sequencing, gVCF is also an appropriate choice to represent and compress the
results.
gVCF is a text file format, stored as a gzip compressed file (*.genome.vcf.gz).
Compression is further achieved by joining contiguous nonvariant regions with similar
properties into single ‘block’ VCF records. To maximize the utility of gVCF, especially for
high stringency applications, the properties of the compressed blocks are conservative.
Block properties like depth and genotype quality reflect the minimum of any site in the
block. The gVCF file can be indexed (creating a *.tbi file) and used with existing VCF
tools such as tabix and IGV, making it convenient both for direct interpretation and as a
starting point for further analysis.
For more information, see sites.google.com/site/gvcftools/home/about-gvcf.
When to use it
Use it for direct interpretation or as a starting point for further analysis with downstream
analysis that is compatible with gVCF, such as tabix and IGV.
When not to use it
Do not use it with tools that are not compatible with the gVCF format.
How to use it
Apps that use gVCF files find it when kicked off and directed to the sample. If using
gVCF files in other tools, download the file to use it in the outside tool.
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The following conventions are used in the variant caller gVCF files.
Samples per File
There is only one sample per gVCF file.
Nonvariant Blocks Using END Key
Contiguous nonvariant segments of the genome can be represented as single records in
gVCF. These records use the standard 'END' INFO key to indicate the extent of the
record. Even though the record can span multiple bases, only the first base is provided
in the REF field to reduce file size.
The following is a simplified segment of a gVCF file, describing a segment of nonvariant
calls (starting with an A) on chromosome 1 from position 51845 to 51862.
##INFO=<ID=END,Number=1,Type=Integer,Description="End position
of the variant described in this record">#CHROM POS ID REF
ALT QUAL FILTER INFO FORMAT NA19238chr1 51845 . A . . PASS
END=51862
Any field provided for a block of sites, such as read depth (using the DP key), shows the
minimum value that is observed among all sites encompassed by the block. Each
sample value shown for the block, such as the depth (DP), is restricted to a range where
the maximum value is within 30% or 3 of the minimum. For example, for sample value
range [x,y], y <= x+max(3,x*0.3). This range restriction applies to each of the sample
values printed in the final block record.
Indel Regions
Sites that are "filled in" inside deletions have additional changes:
All deletions:
} Sites inside any deletion are marked with the deletion filters, in addition to any
filters that have already been applied to the site.
} Sites inside deletions cannot have a genotype or alternate allele quality score higher
than the corresponding value from the enclosing indel.
Heterozygous deletions:
} Sites inside heterozygous deletions are altered to have haploid genotype entries (eg,
"0" instead of "0/0", "1" instead of "1/1").
} Heterozygous SNV calls inside heterozygous deletions are marked with the
"SiteConflict" filter and their genotype is unchanged.
Homozygous deletions:
} Homozygous reference and no-call sites inside homozygous deletions have genotype
"."
} Sites inside homozygous deletions that have a nonreference genotype are marked
with a “SiteConflict” filter, and their genotype is unchanged.
} Site and genotype quality are set to "."
The described modifications reflect the notion that the site confidence is bound within
the enclosing indel confidence.
On occasion, the variant caller produces multiple overlapping indel calls that cannot be
resolved into 2 haplotypes. If this case, all indels and sites in the region of the overlap
are marked with the IndelConflict filter.
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Detailed Description
Genotype Quality for Variant and Nonvariant Sites
The gVCF file uses an adapted version of genotype quality for variant and nonvariant
site filtration. This value is associated with the key GQX. The GQX value is intended to
represent the minimum of {Phred genotype quality assuming the site is variant, Phred
genotype quality assuming the site is nonvariant}. The reason for using this value is to
allow a single value to be used as the primary quality filter for both variant and
nonvariant sites. Filtering on this value corresponds to a conservative assumption
appropriate for applications where reference genotype calls must be determined at the
same stringency as variant genotypes, ie:
} An assertion that a site is homozygous reference at GQX >= 30 is made assuming the
site is variant.
} An assertion that a site is a nonreference genotype at GQX >= 30 is made assuming
the site is nonvariant.
Section Descriptions
The gVCF file contains the following sections:
} Metainformation lines start with ## and contain metadata, config information, and
define the values that the INFO, FILTER, and FORMAT fields can have.
} The header line starts with # and names the fields that the data lines use. These
fields are #CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, followed
by one or more sample columns.
} Data lines that contain information about one or more positions in the genome.
If you extract the variant lines from a gVCF file, you produce a conventional variant VCF
file.
Field Descriptions
The fixed fields #CHROM, POS, ID, REF, ALT, QUAL are defined in the VCF 4.1
standard provided by the 1000 Genomes Project. The fields ID, INFO, FORMAT, and
sample are described in the metainformation.
} CHROM: Chromosome: an identifier from the reference genome or an anglebracketed ID String ("<ID>") pointing to a contig.
} POS: Position: The reference position, with the first base having position 1. Positions
are sorted numerically, in increasing order, within each reference sequence CHROM.
There can be multiple records with the same POS. Telomeres are indicated by using
positions 0 or N+1, where N is the length of the corresponding chromosome or
contig.
} ID: Semicolon separated list of unique identifiers where available. If this ID is a
dbSNP variant, it is encouraged to use the rs number. No identifier is present in
more than 1 data record. If there is no identifier available, then the missing value is
used.
} REF: Reference bases: A,C,G,T,N; there can be multiple bases. The value in the POS
field refers to the position of the first base in the string. For simple insertions and
deletions in which either the REF or 1 of the ALT alleles would otherwise be
null/empty, the REF and ALT strings include the base before the event. This
modification is reflected in the POS field. The exception is when the event occurs at
position 1 on the contig, in which case they include the base after the event. If any of
the ALT alleles is a symbolic allele (an angle-bracketed ID String "<ID>"), the
padding base is required. In that case, POS denotes the coordinate of the base
preceding the polymorphism.
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}
}
}
}
}
ALT: Comma-separated list of alternate nonreference alleles called on at least 1 of the
samples. Options are:
} Base strings made up of the bases A,C,G,T,N
} Angle-bracketed ID String (”<ID>”)
} Break-end replacement string as described in the section on break-ends.
If there are no alternative alleles, then the missing value is used.
QUAL: Phred-scaled quality score for the assertion made in ALT. ie -10log_10
probability (call in ALT is wrong). If ALT is ”.” (no variant), this score is -10log_10 p
(variant). If ALT is not ”.”, this score is -10log_10 p(no variant). High QUAL scores
indicate high confidence calls. Although traditionally people use integer Phred
scores, this field is permitted to be a floating point to enable higher resolution for low
confidence calls if desired. If unknown, the missing value is specified. (Numeric)
FILTER: PASS if this position has passed all filters, ie a call is made at this position.
Otherwise, if the site has not passed all filters, a semicolon-separated list of codes for
filters that fail. gVCF files use the following values:
} PASS: position has passed all filters.
} IndelConflict: Locus is in region with conflicting indel calls.
} SiteConflict: Site genotype conflicts with proximal indel call, which is typically a
heterozygous SNV call made inside a heterozygous deletion.
} LowGQX: Locus GQX (minimum of {Genotype quality assuming variant
position,Genotype quality assuming nonvariant position}) is less than 30 or not
present.
} HighDPFRatio: The fraction of base calls filtered out at a site is greater than 0.3.
} HighSNVSB: SNV strand bias value (SNVSB) exceeds 10. High strand bias
indicates a potential high false-positive rate for SNVs.
} HighSNVHPOL: SNV contextual homopolymer length (SNVHPOL) exceeds 6.
} HighREFREP: Indel contains an allele that occurs in a homopolymer or
dinucleotide track with a reference repeat greater than 8.
} HighDepth: Locus depth is greater than 3x the mean chromosome depth.
INFO: Additional information. INFO fields are encoded as a semicolon-separated
series of short keys with optional values in the format: <key>=<data>[,data]. gVCF
files use the following values:
} END: End position of the region described in this record.
} BLOCKAVG_min30p3a: nonvariant site block. All sites in a block are constrained
to be nonvariant, have the same filter value, and have all sample values in range
[x,y], y <= max(x+3,(x*1.3)). All printed site block sample values are the minimum
observed in the region spanned by the block.
} SNVSB: SNV site strand bias.
} SNVHPOL: SNV contextual homopolymer length.
} CIGAR: CIGAR alignment for each alternate indel allele.
} RU: Smallest repeating sequence unit extended or contracted in the indel allele
relative to the reference. If longer than 20 bases, RUs are not reported.
} REFREP: Number of times RU is repeated in reference.
} IDREP: Number of times RU is repeated in indel allele.
FORMAT: Format of the sample field. FORMAT specifies the data types and order of
the subfields. gVCF files use the following values:
} GT: Genotype.
} GQ: Genotype Quality.
} GQX: Minimum of {Genotype quality assuming variant position, Genotype quality
assuming nonvariant position}.
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}
}
} DP: Filtered base call depth used for site genotyping.
} DPF: Base calls filtered from input before site genotyping.
} AD: Allelic depths for the ref and alt alleles in the order listed. For indels, this
value only includes reads that confidently support each allele (posterior
probability 0.999 or higher that read contains indicated allele vs all other
intersecting indel alleles).
} DPI: Read depth associated with indel, taken from the site preceding the indel.
SAMPLE: Sample fields as defined by the header.
VCF Files
What is it?
VCF is a text file format that contains information about variants found at specific
positions in a reference genome. The file format consists of metainformation lines, a
header line, and then data lines. Each data line contains information about a single
variant.
When to use it
Use it for direct interpretation or as a starting point for further analysis with downstream
analysis that is compatible with VCF, such as IGV or the UCSC Genome Browser.
When not to use it
Do not use it with tools that are not compatible with the VCF format.
NOTE
Windows recognizes VCF files as an Outlook contact file. Do not open VCF files in
Outlook.
How to use it
If you use an app in BaseSpace that uses VCF files as input, the app locates the file when
launched. If using VCF files in other tools, download the file to use it in the external tool.
Detailed Description
The file naming convention for VCF files is as follows: SampleName_S#.vcf (where # is
the sample number determined by ordering in the sample sheet).
The header of the VCF file describes the tags used in the remainder of the file and has
the column header:
##fileformat=VCFv4.1
##fileDate=20120317
##source=SequenceAnalysisReport.vshost.exe
##reference=
##phasing=none
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=TI,Number=.,Type=String,Description="Transcript ID">
##INFO=<ID=GI,Number=.,Type=String,Description="Gene ID">
##INFO=<ID=CD,Number=0,Type=Flag,Description="Coding Region">
##FILTER=<ID=q20,Description="Quality below 20">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype
Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
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Setting
Description
ALT
The alleles that differ from the reference read. For example, an insertion of a
single T could show reference A and alternate AT.
CHROM
The chromosome of the reference genome. Chromosomes appear in the same
order as the reference FASTA file (generally karyotype order)
FILTER
If all filters are passed, the' PASS' is written. The possible filters are as follows:
• q20 – The variant score is less than 20. (Configurable using the
VariantFilterQualityCutoff setting in the config file)
• r8 – For an Indel, the number of repeats in the reference (of a 1- or 2-base
repeat) is greater than 8. (Configurable using the IndelRepeatFilterCutoff
setting in the config file)
FORMAT
The format column lists fields (separated by colons), for example, "GT:GQ". The
list of fields provided depends on the variant caller used. The available fields are
as follows:
AD – Entry of the form X,Y where X is the number of reference calls, Y the
number of alternate calls
GQ – Genotype quality
GT – Genotype. 0 corresponds to the reference base, 1 corresponds to the first
entry in the ALT column, 2 corresponds to the second entry in the ALT column,
and so on. The '/' indicates that there is no phasing information.
NL – Noise level; an estimate of base calling noise at this position
SB – Strand bias at this position. Larger negative values indicate more bias;
values near 0 indicate little strand bias.
VF – Variant frequency. The percentage of reads supporting the alternate allele.
ID
The rs number for the SNP obtained from dbSNP. If there are multiple rs
numbers at this location, the list is semicolon delimited. If no dbSNP entry exists
at this position, the missing value ('.') is used.
INFO
The possible entries in the INFO column:
• AD – Entry of the form X,Y where X is the number of reference calls, Y the
number of alternate calls.
• CD – A flag indicating that the SNP occurs within the coding region of at least 1
RefGene entry
• DP – The depth (number of base calls aligned to this position)
• GI – A comma-separated list of gene IDs read from RefGene
• NL – Noise level; an estimate of base calling noise at this position.
• TI – A comma-separated list of transcript IDs read from RefGene
• SB – Strand bias at this position.
• VF – Variant frequency. The number of reads supporting the alternate allele.
POS
The 1-based position of this variant in the reference chromosome. The
convention for VCF files is that, for SNPs, this base is the reference base with the
variant. For indels or deletions, this base is the reference base immediately
before the variant. Variants are in order of position.
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A sample line of the VCF file, with the data that is used to populate each column
described:
chr22 16285888 rs76548004 T C 17 d15;q20 DP=11;TI=NM_
001136213;GI=POTEH;CD GT:GQ 1/0:17
Setting
Description
QUAL
A Phred-scaled quality score assigned by the variant caller. Higher scores
indicate higher confidence in the variant (and lower probability of errors). For a
quality score of Q, the estimated probability of an error is 10-(Q/10). For
example, the set of Q30 calls has a 0.1% error rate. Many variant callers assign
quality scores (based on their statistical models) which are high relative to the
error rate observed in practice.
REF
The reference genotype. For example, a deletion of a single T can read reference
TT and alternate T.
SAMPLE
The sample column gives the values specified in the FORMAT column. One
MAXGT sample column is provided for the normal genotyping (assuming the
reference). For reference, a second column is provided for genotyping assuming
the site is polymorphic. See the Starling documentation for more details.
FASTQ Files
What is it?
BaseSpace Onsite converts *.bcl files into FASTQ files, which contain base call and
quality information for all reads passing filtering.
When to use it.
FASTQ files can be used as sequence input for alignment and other secondary analysis
software.
When not to use it.
Do not use it with tools that are not compatible with the FASTQ format.
How to use it
BaseSpace Onsite automatically generates FASTQ files in sample sheet-driven workflow
apps. Other apps that perform alignment and variant calling also automatically use
FASTQ files.
Naming
FASTQ files are named with the sample name and the sample number, which is a
numeric assignment based on the order that the sample is listed in the sample sheet.
Example:
} SampleName—The sample name provided in the sample sheet. If a sample name is
not provided, the file name includes the sample ID, which is a required field in the
sample sheet and must be unique.
} S1—The sample number based on the order that samples are listed in the sample
sheet starting with 1. In this example, S1 indicates that this sample is the first
sample listed in the sample sheet.
NOTE
Reads that cannot be assigned to any sample are written to a FASTQ file for sample
number 0, and excluded from downstream analysis.
}
38
L001—The lane number.
Document # 1000000002666 v00
}
R1—The read. In this example, R1 means Read 1. For a paired-end run, there is at
least one file with R2 in the file name for Read 2. When generated, index reads are I1
or I2.
001—The last segment is always 001.
Compression
FASTQ files are saved compressed in the GNU zip format (an open source file
compression program), indicated by the .gz file extension.
Format
Each entry in a FASTQ file consists of 4 lines:
} Sequence identifier
} Sequence
} Quality score identifier line (consisting only of a +)
} Quality score
@<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<xpos>:<y-pos>:<UMI> <read>:<is filtered>:<control
number>:<index>
The following table describes the elements.
Element
Requirements Description
@
@
Each sequence identifier line starts with @.
<instrument> Characters
Instrument ID.
allowed:
a–z, A–Z, 0–9
and
underscore
<run number> Numerical
Run number on instrument.
<flowcell
Characters
ID>
allowed:
a–z, A–Z, 0–9
<lane>
Numerical
Lane number.
<tile>
Numerical
Tile number.
<x_pos>
Numerical
X coordinate of cluster.
<y_pos>
Numerical
Y coordinate of cluster.
<UMI>
Restricted
Optional, appears when UMI is specified in sample sheet.
characters:
UMI sequences for Read 1 and Read 2, seperated by a
A/T/G/C/N
plus [+].
<read>
Numerical
Read number. 1 can be single read or Read 2 of pairedend.
<is
Y or N
Y if the read is filtered (did not pass), N otherwise.
filtered>
<control
Numerical
0 when none of the control bits are on, otherwise it is an
number>
even number.
<index>
Restricted
Index of the read.
characters:
A/T/G/C/N
An example of a valid entry is as follows; note the space preceding the read number
element:
@SIM:1:FCX:1:15:6329:1045:GATTACT+GTCTTAAC 1:N:0:ATCCGA
TCGCACTCAACGCCCTGCATATGACAAGACAGAATC
+
<>;##=><9=AAAAAAAAAA9#:<#<;<<<????#=
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}
Quality Scores
A quality score (or Q-score) expresses an error probability. In particular, it serves as a
convenient and compact way to communicate small error probabilities.
Given an assertion, A, the quality score, Q(A), expresses the probability that A is not true,
P(~A), according to the relationship:
Q(A) =-10 log10(P(~A))
where P(~A) is the estimated probability of an assertion A being wrong.
The relationship between the quality score and error probability is demonstrated with the
following table.
Quality score, Q(A)
10
20
30
Error probability, P(~A)
0.1
0.01
0.001
NOTE
On the systems we currently support, Q-scores are automatically binned. The specific
binning applied depends on the current Q-table. See the white paper Reducing Whole
Genome Data Storage Footprint for more information, available from www.illumina.com.
Quality Scores Encoding
In FASTQ files, quality scores are encoded into a compact form, which uses only 1 byte
per quality value. In this encoding, the quality score is represented as the character with
an ASCII code equal to its value + 33. The following table demonstrates the relationship
between the encoding character, its ASCII code, and the quality score represented.
NOTE
When Q-score binning is in use, the subset of Q-scores applied by the bins is displayed.
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Table 1 ASCII Characters Encoding Q-scores 0–40
Symbol
ASCII Code
QScore
Symbol
ASCII Code
QScore
!
33
0
6
54
21
"
34
1
7
55
22
#
35
2
8
56
23
$
36
3
9
57
24
%
37
4
:
58
25
&
38
5
;
59
26
'
39
6
<
60
27
(
40
7
=
61
28
)
41
8
>
62
29
*
42
9
?
63
30
+
43
10
@
64
31
,
44
11
A
65
32
-
45
12
B
66
33
.
46
13
C
67
34
/
47
14
D
68
35
0
48
15
E
69
36
1
49
16
F
70
37
2
50
17
G
71
38
3
51
18
H
72
39
4
52
19
I
73
40
5
53
20
Health Runs
A user can choose whether to send anonymous system health information to Illumina.
Health runs help Illumina diagnose issues and improve our products. The information
consists of InterOp files and log files, and is not tied to any user account. This option is
on by default.
Share Data
Data in BaseSpace Onsite can be shared with collaborators in a couple of different ways.
You can either share data at a run or project level, via an email invitation or through a
hyperlink. With the email invitation option, only the accounts with the specified email
can view shared data. Sharing via a hyperlink option allows anyone with access to the
hyperlink to be able to view the shared data, as long as the hyperlink is still active.
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Sharing is for read-only access. If you want a collaborator to have write access, see
Transfer Owner on page 46.
NOTE
Runs and projects have separate permissions. If you share a run, the project associated
with that run is not shared automatically. Therefore, samples and app results are not
accessible to collaborators of the run.
The following topics describe how to share data.
} Share a Project using the Get Link option on page 42
} Share a Project Using the Email Option on page 42
} Share a Run with Get Link on page 43
} Share a Run Using the Email Option on page 43
Share a Project using the Get Link option
The hyperlink can be turned on or off by setting the activate or deactivate option. Anyone
can access the project or run when the link is activated. Furthermore, anyone who
previously accepted the link still has access to the run even when the link is deactivated.
Use the Get Link option when you do not want to assign a project to a specific person.
However, do not use this option if you want to confine the list of who has access to the
project.
NOTE
If you want more control, use the email share option to specify who can view the project.
SeeShare a Project Using the Email Option on page 42.
To use the Get Link option, perform the following steps.
1
Click the Projects icon.
2
Click the desired project.
3
Click the Get Link button.
4
Click the Activate button.
5
Copy the URL to share with collaborators.
The link is active until the Deactivate option is selected. To deactivate a link, perform the
following steps.
6
Navigate to the shared item.
7
Click the Get Link button.
8
Click the Deactivate button.
Share a Project Using the Email Option
Use the Share Project option to share a Project using an email link. The specified
collaborators receive an email with a link to the Project and only that person can view
the corresponding data.
The email option allows greater control over who can view your data. Sharing using the
Get Link options gives anyone access to your data, as long as the link is left activated.
To email a link, perform the following steps.
42
1
Click the Projects icon.
2
Click the desired project.
3
Click Share Project.
Document # 1000000002666 v00
In the Share Settings dialog box, enter the collaborators email address, and then click
Invite.
NOTE
The invitation email address must match your BaseSpace Onsite login email address.
Otherwise, your collaborator is not able to view the project.
5
Click Save Settings.
Share a Run with Get Link
Sharing using the Get Link option allows you to share a run with any collaborator who
has access to the link. The hyperlink can be turned on or off by setting the activate or
deactivate option. Anyone can access the project or run when the link is activated.
Furthermore, anyone who previously accepted the link still has access to the run even
though the link is deactivated.
Sharing runs with the Get Link option is similar to sharing projects with the Get Link
option.
NOTE
If you want more control, use the email share option to specify who can view the project.
See Share a Run Using the Email Option on page 43.
To share a run using the Get Link option, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
3
Click the More button and select the Get Link option.
4
Click the Activate button.
5
Copy the URL to share with collaborators.
The link is active until the Deactivate option is selected. To deactivate a link, perform the
following steps.
6
Navigate to the run
7
Click the Get Link button.
8
Click the Deactivate button.
NOTE
Runs and projects have separate permissions. If you share a run, the project associated
with that run is not shared automatically. Therefore, samples and app results are not
accessible to collaborators of the run.
Share a Run Using the Email Option
Use the Share Project option to share a Run with a specified collaborator via an email
link. The specified collaborators receive an email with a link to the Run and only that
person can view the corresponding data.
The email option allows greater control over who can view your data. Sharing using the
Get Link options gives anyone access to your data, as long as the link is left activated.
To email a link, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
3
Click Share.
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4
4
In the Share Settings dialog box, enter the collaborators email address, and then click
Invite.
NOTE
The invitation email address must match your BaseSpace Onsite login email address.
Otherwise, your collaborator is not able to view the project.
5
Click Save Settings.
NOTE
Runs and projects have separate permissions. If you share a run, the project associated
with that run is not shared automatically. Therefore, samples and app results are not
accessible to collaborators of the run.
Project and Sample Management
The following topics describe how to manage projects and samples in BaseSpace Onsite.
} Combine Samples on page 44
} Transfer Owner on page 46
Edit Project Details
Use the Edit Project option to change details regarding the project, such as the
description or project name.
To edit a project, perform the following steps.
1
Click the Projects icon.
2
Click the desired project.
3
Click Edit Project.
4
Change project details in the Edit Project dialog box.
5
Click Save.
Set Up a New Project
The following list includes reasons to set up a new project.
} To analyze a sample in the context of 2 different projects
} To transfer ownership of samples to a collaborator, but still keep a copy yourself
} To split a project into multiple projects
To set up a new project, perform the following steps.
1
Click the Projects icon.
2
Click New Project in the top left corner.
3
Enter a new name and description.
4
Click Create.
To copy samples into the new project, see Copy Samples on page 45.
Combine Samples
Use the following method to combine the data from 2 or more different sequencing runs
on the same sample. You can only combine samples that have the same read lengths.
To combine samples, perform the following steps.
44
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Click the Projects icon.
2
Click the desired project.
3
Click the Samples link from the left navigation menu.
4
Select the checkboxes of the samples you want to combine.
5
Click Combine.
6
Click Combine in the pop-up screen.
Copy Samples
You can copy samples from a project to another project for the following reasons:
} To analyze a sample in the context of 2 different projects
} To transfer ownership of samples to a collaborator, but still keep a copy yourself
} To assign a sample to the correct project
To copy samples, perform the following steps.
1
Click the Projects icon.
2
Click the desired project.
3
Click the Samples link from the left navigation menu.
4
Select the checkboxes of the samples you want to copy.
5
Click Copy.
6
Select the new project in the drop-down list.
7
Click the Copy button.
Upload Files
Some apps need additional files generated outside of BaseSpace Onsite. Some appls also
provide downstream analysis for results generated outside of BaseSpace Onsite.
To upload files, perform the following steps.
1
Click the Projects icon.
2
Go to the project you want to add the file to.
NOTE
You can only upload files to projects you own.
3
Click Import.
4
Select the file to upload using 1 of the following methods:
} Drag and drop the file in the Drag and Drop box.
} Browse to the file through the select file link and click Open.
5
BaseSpace Onsite now uploads the file to your project.
6
Enter the analysis name in the Name of analysis box.
7
[Optional] Associate the file you are importing with the samples used as inputs. By
making this association, the analysis is listed on the sample detail page. You can
also locate these uploaded files later by navigating to 1 of the samples.
8
Click Complete Import.
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1
FASTQ File Upload Requirements
The FASTQ file is a text format file used to represent sequences. Each record has 4 lines.
The 4 lines of data are an identifier (read descriptor), the sequence, +, and the quality
scores. For a detailed description of the FASTQ format, see FASTQ Files on page 38.
Make sure that the FASTQ file adheres to the following upload requirements:
} The uploader only supports gzipped FASTQ files generated on Illumina instruments
} The name of the FASTQ files conforms to the following convention:
SampleName_SampleNumber_Lane_Read_FlowCellIndex.fastq.gz
For example,
SampleName_S1_L001_R1_001.fastq.gz
SampleName_S1_L001_R2_001.fastq.gz)
} The read descriptor in the FASTQ files conforms to the following convention:
@Instrument:RunID:FlowCellID:Lane:Tile:X:Y
ReadNum:FilterFlag:0:SampleNumber:
For example, a Read 1 descriptor could look like this line:
@M00900:62:000000000-A2CYG:1:1101:18016:2491 1:N:0:13
And the corresponding Read 2 would have a 2 in the ReadNum field:
@M00900:62:000000000-A2CYG:1:1101:18016:2491 2:N:0:13
Quality considerations:
} The number of base calls for each read equals the number of quality scores.
} The number of entries for Read 1 equals the number of entries for Read 2.
} The uploader determines whether files are paired-end based on matching file names
in which the only difference is the ReadNum.
} For paired-end reads, the descriptor must match for every entry for both reads 1 and
2.
} Each read has passed filter.
The uploader rejects any upload session containing files that do not meet the
requirements. If a file is rejected, a message is provided. This message states why the
upload failed and what to do to remedy the problem.
Transfer Owner
You can use the Transfer Owner option to hand control of data over to a collaborator or
customer. You can use this option for the following reasons:
} To give control of your data to a collaborator. You can only transfer data to
collaborators who have an account on BaseSpace Onsite.
NOTE
If items from a project are in the trash, you cannot transfer ownership of the project.
To use this option, perform the following steps.
1
Select the project or run you want to transfer.
} To transfer a project, perform the following steps.
a
b
c
46
Click the Projects icon.
Click the desired project.
Click the Transfer Owner button.
Document # 1000000002666 v00
a
b
c
Click the Runs icon.
Click the desired run.
Click the More button, and then select Transfer Ownership.
2
Enter new owner email and an optional message in the Transfer Ownership dialog
box.
3
Click Continue.
Delete Items
You can delete items in a 2-step process:
1
Move the item to trash.
2
Clean up the trash.
For more information, see the following topics.
} Delete Run on page 47
} Delete Project on page 47
} Delete Analysis on page 48
} Delete Sample on page 48
} Empty Trash on page 49
} Restore Trash on page 49
Delete Run
To move a project out of your Runs list into the trash, perform the following steps.
1
Click the Runs icon.
2
Click the desired run.
3
Click Move to Trash.
4
If there are analyses or samples associated with this run, BaseSpace Onsite asks if
you also want to delete those analyses and samples. Select the checkbox if you want
to delete the associated items.
5
Click Confirm.
If you are the owner of the run, the run now appears in the trash.
You can permanently delete the run from trash by emptying all items in the trash;
see Empty Trash on page 49 You can also restore the run to its original location; see
Restore Trash on page 49.
Note the following items about deleting a run:
} If you received the run as a share, the deleted run does not appear in the trash. If you
want to restore a run shared with you, click the previously sent share link or contact
the owner.
} Runs cannot be removed if they are in a nonterminal state (eg, running, uploading,
or analyzing).
} Do not perform this action if you want to archive a run.
Delete Project
To move a project out of your Projects list into the trash, perform the following steps.
1
Click the Projects icon.
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How To Use BaseSpace Onsite
} To transfer a run, perform the following steps.
2
Click the desired project.
3
Click Move to Trash.
4
Click Confirm.
If you are the owner of the project, the project now appears in the trash.
You can permanently delete it from trash by emptying all items in the trash; see
Empty Trash on page 49 You can also restore the project to its original location; see
Restore Trash on page 49.
Note the following items about deleting a project:
} If you received the project as a share, the deleted project does not appear in the trash.
If you want to restore a project shared with you, click the previously sent share link
or contact the owner.
} Do not perform this action if you want to archive a project.
Delete Analysis
To move an analysis out of your Analysis Results list into the trash, perform the
following steps.
1
Click the Projects icon.
2
Click the desired project.
3
Select the analysis results to be deleted.
4
Click Move to Trash.
5
Click Confirm.
The analysis is now in the trash.
You can permanently delete the analysis from BaseSpace Onsite by emptying all
items in the trash; see Empty Trash on page 49. You can also restore the analysis to
its original location; see Restore Trash on page 49.
Note the following items about deleting an analysis result:
} You cannot delete an analysis that is in a nonterminal state (eg, pending execution
or running).
} Deleting an analysis from a project that is in ownership transfer can cause a delay
until the transfer has completed.
} Do not perform this action if you want to archive an analysis result.
Delete Sample
To move a sample out of your Samples list into the trash, perform the following steps.
48
1
Click the Projects icon.
2
Click the desired project.
3
Click the Samples tab on the left navigation bar.
4
Select the samples to be deleted.
5
Click Move to Trash.
6
Click Confirm.
The sample is now in the trash.
You can permanently delete the sample from BaseSpace Onsite by emptying all
items in the trash; see Empty Trash on page 49. You can also restore the analysis to
its original location; see Restore Trash on page 49.
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Empty Trash
After you have deleted an item, it is present in the Trash if you are the owner of that
item. With this method, you can delete all items in the trash from BaseSpace Onsite
permanently.
To delete an item from BaseSpace Onsite permanently, perform the following steps.
1
Click View Trash.
2
Click Empty Trash.
3
Click Confirm.
The items are now ready to be purged from BaseSpace Onsite by the admin; see
Purge Deleted Items on page 53.
Restore Trash
After you have deleted an item, it is present in the Trash if you are the owner of that
item. To restore an item from the trash to its original location, perform the following
steps.
1
Click View Trash.
2
Select the items you want to restore.
3
Click Restore Trash.
The item is now restored to its original location. Restored items keep all their original
attributes except for the share recipients.
Fix Sample Sheet / Rerun Workflow
The Fix Sample Sheet page lets you correct errors in your sample sheet for HiSeq runs, or
set up a new analysis to requeue. Use this feature for the following reasons:
} To fix errors in the sample sheet—Errors in the sample sheet can prevent BaseSpace
Onsite from processing a run. This option allows BaseSpace Onsite to finish the
analysis.
} To change analysis parameters—If first analysis is suboptimal, you can resubmit the
sample sheet and requeue the run with new analysis parameters one time.
} To change indexing details—If index settings for samples were wrong, you can
correct the settings.
NOTE
You can only submit a corrected sample sheet and requeue the run 1 time.
To fix a sample sheet and rerun a workflow, perform the following steps.
1
Open the Fix Sample Sheet page using 1 of the following methods:
} If a run has a Needs Attention state, open the run and click Fix Sample Sheet.
} Go to a run, click the More drop-down list, and then select Fix Sample Sheet.
The Fix Sample Sheet page opens. If BaseSpace Onsite has detected an error, it shows
the issue above the black sample sheet editor.
2
Make changes depending on the complexity of the change:
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Note the following items about deleting a sample:
} If you received the sample as a share, the deleted sample does not appear in the
trash. If you want to restore a sample shared with you, click the previously sent
share link or contact the owner.
} Do not perform this action if you want to archive a sample.
} Easy fix—Edit the sample sheet in the sample sheet editor. BaseSpace Onsite keeps
validating the sample sheet as you edit; any remaining issues are displayed above
the sample sheet editor.
} Complex Fix—Use Illumina Experiment Manager (IEM) to create a sample sheet.
a
b
c
3
If necessary, install IEM and open the program.
Import the original sample sheet from your system in IEM and edit it, or
generate a new sample sheet. For more information, see the Illumina
Experiment Manager User Guide (part # 15031335).
Copy and paste the sample sheet into the Sample Sheet Editor in BaseSpace
Onsite.
BaseSpace Onsite validates the sample sheet; any issues are displayed above
the sample sheet editor.
When you are done editing and the sample sheet is valid, click the Queue Analysis
button.
BaseSpace Onsite starts analyzing the run using the new sample sheet.
You can only resubmit a sample sheet and requeue the run 1 time.
NOTE
If your edits result in an invalid sample sheet, the Queue Analysis button is not available.
You can return to the original using the Load Original button.
Common Sample Sheet Fixes
If a sample sheet is invalid, it could be because the genome path is not set up correctly.
This situation is indicated through the Genome Path Unknown Genome warning (as in the
example). The paths of the standard BaseSpace Onsite genomes have to conform to the
following relative paths:
Arabidopsis_thaliana\NCBI\build9.1\Sequence\WholeGenomeFASTA
Bos_taurus\Ensembl\UMD3.1\Sequence\WholeGenomeFASTA
Escherichia_coli_K_12_DH10B\NCBI\2008-0317\Sequence\WholeGenomeFASTA
Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA
Mus_musculus\UCSC\mm9\Sequence\WholeGenomeFASTA
PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA
Rattus_norvegicus\UCSC\rn4\Sequence\WholeGenomeFASTA
Saccharomyces_cerevisiae\UCSC\sacCer2\Sequence\WholeGenomeFASTA
Staphylococcus_aureus_NCTC_8325\NCBI\2006-0213\Sequence\WholeGenomeFASTA
Search for Runs, Projects, Samples, Files, and Apps
The Search function allows you to find runs, projects, samples, files, and apps.
50
1
Click the search icon.
2
Type in the run, project, or sample name in the search field and hit enter.
3
Select the desired run, project, sample, file, or app in the search results. You can also
filter the search results by these categories using the drop-down list at the right of the
results page.
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The admin of BaseSpace Onsite has the following tasks:
} Manage analysis, notifications, storage, users, system health, planned runs, software
updates, and alarms using the Admin Panel. For more information, see Manage
BaseSpace Onsite on page 51.
} Replace hard drive or power supply. For more information, see Replacement
Procedures on page 54.
In addition, BaseSpace Onsite sends an email alert if there is an issue with your system.
Error Codes on page 56 provides a list of possible codes and descriptions to help you
troubleshoot.
Manage BaseSpace Onsite
If you have admin privileges, the Account drop-down list provides access to the Admin
Panel. The Admin Panel allows you to manage analysis, notifications, storage, users,
system health, planned runs, software updates, and alarms.
Manage Analysis
On the Analysis page, you see the analyses that are currently running, and the analyses
that are queued. You can sort the analyses by the column headers.
You can perform the following actions:
} Select an active analysis and click Stop to stop the analysis.
} Select a queued analysis and click Remove to remove the analysis from the queue.
} Click Settings to set the administrator notifications you get through email.
Manage Storage
The Storage page contains 3 tabs:
} Active Storage—Provides an overview of the total amount of active storage used and
free, and the storage by user. Active samples, runs, and analyses are stored on the
BaseSpace Onsite system, and can be used for analysis. At the bottom, you see the
list of active samples, runs, and analyses stored; you can sort this list by clicking the
column headers. Any changes that add or remove data usually take 3–5 minutes to
be reflected in the pie chart. Active samples, runs and analyses are stored on the
BaseSpace Onsite system, and can be used for analysis.
NOTE
If there are many merged samples and copied samples on the system, the usage peruser values are overestimated in the Storage Use By Owners pie chart. The Total
Active Storage is not affected.
}
}
Archive Storage—Provides an overview of the archived analyses. Archived samples,
runs, and analyses are stored on the archive system, and cannot be used for analysis
on BaseSpace Onsite without restoring. At the bottom, you see the list of archived
samples, runs, and analyses; you can sort this list by clicking the column headers.
Deleted Items—Provides an overview of the items that have been deleted. At the
bottom, you see the list of deleted samples, runs, and analyses; you can sort this list
by clicking the column headers. You can restore these items to active storage, or
purge them from BaseSpace Onsite, which deletes them permanently.
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Admin Tasks
NOTE
Illumina highly recommends that you set up an archive location.
Archive or Backup Analysis
To archive or backup an analysis, perform the following steps.
1
On the Storage page, go to the Archive Storage tab.
2
Select the analysis.
3
Click Archive.
4
A dialog box appears, asking you if you want to keep the data in active storage.
} If you keep the data in active storage, you can keep working with the analysis,
while making a backup in the archive.
} If you do not keep the analysis in active storage, the data are archived, and you
cannot work with the analysis in BaseSpace Onsite. You can always move it back
to active storage as described in Restore Analysis From Archive on page 52.
The maximum speed for archiving is 25 Mb/s, so it does not interfere with other
BaseSpace Onsite tasks.
Restore Analysis From Archive
To restore an analysis from archive to active status, perform the following steps.
1
On the Storage page, go to the Archive Storage tab.
2
Select the analysis.
3
Click Unarchive.
If there is sufficient free space, BaseSpace Onsite restores the analysis. If there is not
enough space, BaseSpace Onsite displays an error message.
NOTE
You cannot restore an archived item that has been deleted and purged from BaseSpace
Onsite.
Set Up Archive Location
To set up an archive location, perform the following steps.
1
On the Storage page, go to the Archive Storage tab.
2
Click Mount
3
Fill out the form.
You can set up 1 archive location per BaseSpace Onsite system.
Restore Deleted Item
To restore a deleted item to active status, perform the following steps.
52
1
On the Storage page, go to the Deleted Items tab.
2
Select the analysis.
3
Click Unarchive.
If there is sufficient free space, BaseSpace Onsite restores the item. If there is not
enough space, BaseSpace Onsite displays an error message.
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To purge deleted items from BaseSpace Onsite permanently, perform the following:
1
On the Storage page, go to the Deleted Items tab.
2
Click Purge.
This action removes all items in the trash from BaseSpace Onsite permanently.
Storage Check
BaseSpace Onsite has limited storage capacity, and checks the free space available before
uploading a run or starting an app. The necessary space is then reserved until the
process completes.
If there is not enough space, you see an error message and the run or app does not start.
If the space check fails before starting FASTQ generation, the run gets into Needs
Attention state. To manage available space, see Archive or Backup Analysis on page 52.
Manage Users
On the Users page, you see a list of current BaseSpace Onsite accounts, and their roles.
You can sort the users by the column headers.
To set up a new user, click Add User and fill out the form.
The new user gets an email with a link to set up a new password. If the user does not get
an email, the user can go to the BaseSpace Onsite login page and click Forgot Password
to resend the email.
If you did not configure SMTP during install, be aware of the following items:
} You enter the password for the new user.
} BaseSpace Onsite does not enforce usernames to be in the form of an email, which
can cause a problem with HiSeq integration. Make sure to enforce that all users
create a username in the format of an email.
} If you enable the SMTP support after using BaseSpace Onsite without SMTP support,
all users that are logged in must log out and then log back in. Otherwise, they do not
receive notifications by email or on the dashboard.
Monitor System Health
On the System Health page, you see the BaseSpace Onsite system health alerts. You can
sort the alerts by the column headers.
Many sensors are monitored for health in the BaseSpace Onsite server. If a sensor
indicates a failure, BaseSpace Onsite sends an alert to the administrator. When you
receive an alert, contact Illumina Support to diagnose the error and, if necessary, arrange
a site visit to correct the problem.
Some of these errors, such as a failure of a disk drive or 1 of the power supplies, you can
resolve. See Replacement Procedures on page 54 for instructions. Illumina Support can also
guide you through the process of replacing the faulty component.
If you want to remove an alert, select the alert and click Dismiss.
Unlock Planned Runs
On the Planned Runs page, you see the runs that are currently planned. You can sort the
runs by the column headers.
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Purge Deleted Items
The sequencing system locks planned runs when they are selected. In rare instances, the
sequencing system leaves the run in locked state without starting the run. These runs
must be manually unlocked to access again. Unlocking runs allows the users to edit the
run in the Prep tab, and makes the run available for selection on other sequencing
systems. Unlocking also frees up the reserved run storage space on the BaseSpace Onsite
system.
To unlock a run, select the planned run and click Unlock.
Updates
To update the server software and upload additional genome content, perform the
following steps.
1
Plug the external USB drive with the software update into the BaseSpace Onsite head
node server.
2
Go to the Updates page.
3
Click Detect Drive.
The Updates wizard leads you through the update.
System Logs
The System Logs page provides a download of the log files. You can download all log
files, or packages that contain the system state log files, active analysis log files, or delete
log files.
If an issue arises with your BaseSpace Onsite, Illumina support uses these files to
troubleshoot your system. To speed up troubleshooting, download the appropriate
package before calling Illumina support.
About Page / Licenses
The About page provides a download containing the licenses for third-party software
components.
Manage Alarms on the Settings Page
If there are problems with the hard drive, BaseSpace Onsite sounds a loud alarm. The
Disable Alarm button on the Settings page allows you to turn off a current alarm.
See Replace Hard Drive on page 55 to continue.
CAUTION
Do not disable the alarm and ignore the warning. Failure to address the warning could
lead to irretrievable data loss.
Replacement Procedures
You have received a spare hard drive and power supply module with the instrument. If
needed, you can perform the replacement without calling Illumina, using the instructions
in this section.
To order more, use the following material numbers.
54
Part
Nomenclature
Material Number
Power Supply
Hard drive
PSU 750W 1U CRPS 80PLUS PLATINUM
Hard Drive, 2 TB SATA, 6GB/S
Hard Drive, 4 TB SATA, 6GB/S
10535S
15049450S
20000882
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Admin Tasks
Replace Power Supply Module
To replace the power supply module, perform the following steps.
1
Remove the power cord from the power supply.
2
Press the green and black tab and slide the power supply out.
Figure 2 Slide Power Supply Out
3
Push the new power supply into the slot and make sure that it is seated properly.
Figure 3 Reseat Power Supply
4
Attach the power cord to the power supply.
Replace Hard Drive
To replace the hard drive, perform the following steps.
1
Lift the green tab on hard drive tray, and then pull out the drive.
Figure 4 Lift Tab
BaseSpace Onsite v1.0 LT System Guide
55
Figure 5 Pull Drive Out
2
Look at the label on the drive and check whether it is a 2 TB or 4 TB drive.
3
Remove the 3 screws on each side of the carrier, then remove the old drive from the
carrier.
Figure 6 Remove Drive From Carrier
4
Attach the new drive to the carrier.
5
Insert the new drive into the bay and make sure the tray latches closed.
The new drive is automatically rebuilt.
6
Go to the Settings page in the Admin Panel, and click Enable Alarm.
Data Recovery
To recover data, contact Illumina Technical Support.
Error Codes
If there is an issue with your system, BaseSpace Onsite sends an email alert. The possible
codes and descriptions are listed in this topic to help you troubleshoot.
Error
Code/
Item
ID
56
Item Name
Message
Status
Pwr_
Unit_
Status
Power Unit
Status
The power unit has detected a shutdown
Error
Pwr_
Unit_
Status
Power Unit
Status
The power unit has detected that the system
has been turned on
OK
Document # 1000000002666 v00
Item Name
Message
Status
Pwr_
Unit_
Status
Power Unit
Status
The power unit has detected a loss of AC
power
Error
Pwr_
Unit_
Status
Power Unit
Status
The power unit has detected that the AC
power has been restored
OK
Pwr_
Unit_
Status
Power Unit
Status
The power unit has detected a soft-power
failure
Error
Pwr_
Unit_
Status
Power Unit
Status
The power unit has recovered from a softpower failure
OK
Pwr_
Unit_
Status
Power Unit
Status
The power unit has detected an unexpected
failure
Error
Pwr_
Unit_
Status
Power Unit
Status
The power unit has recovered from an
unexpected failure
OK
PU_$C
Power supply
unit number $C
The power supply is no longer redundant due
to power unit number $C failing
Error
PU_$C
Power supply
unit number $C
The power supply is no longer redundant due
to power unit number $C failing
Error
PU_$C
Power supply
unit number $C
The power supply is no longer redundant due
to power unit number $C failing
Error
PU_$C
Power supply
unit number $C
The power supply is no longer redundant due
to power unit number $C failing
Error
PU_$C
Power supply
unit number $C
The power supply is no longer redundant due
to power unit number $C failing
Error
PU_$C
Power supply
unit number $C
The power supply is no longer redundant due
to power unit number $C failing
Error
PU_$C
Power supply
unit number $C
The power supply is no longer redundant due
to power unit number $C failing
Error
PU_$C
Power supply
unit number $C
The power supply is redundant again
OK
IPMI
IPMI Watchdog
The hardware monitor has detected an
expired timer
Error
IPMI
IPMI Watchdog
The hardware monitor has detected hard
reset of the system
Error
IPMI
IPMI Watchdog
The hardware monitor has detected that the
system is shutting down
Error
BaseSpace Onsite v1.0 LT System Guide
57
Admin Tasks
Error
Code/
Item
ID
58
Error
Code/
Item
ID
Item Name
Message
Status
IPMI
IPMI Watchdog
The hardware monitor has detected that the
system is restarting
Error
IPMI
IPMI Watchdog
The hardware monitor has detected a timer
interrupt
Error
Phy_Sec
Physical Security
The system cover has been opened
Error
Phy_Sec
Physical Security
The system cover has been closed
OK
Phy_Sec
Physical Security
The system has been unplugged from the
network
Error
Phy_Sec
Physical Security
The system network connection has been
restored
OK
FPB
Front Panel
Board
The front panel board has detected a critical
interrupt error
Error
SMI
System Board
Timeout
The system board has detected a timeout
Error
SMI
System Board
Timeout
The system board has recovered from a
timeout
OK
SE
System Event
There was a PEF Action detected
Error
SB
System Board
The system board has detected that the
power button has been pressed
OK
SB
System Board
The system board has detected that the reset
button has been pressed
OK
VR
Voltage
Watchdog
The voltage sensor has detected that the
voltage is not within normal range
Error
VR
Voltage
Watchdog
The voltage sensor has detected that the
voltage is back within normal range
OK
F_$C
Fan number $C
The fans are no longer redundant due to fan
number $C failing
Error
F_$C
Fan number $C
The fans are no longer redundant due to fan
number $C failing
Error
F_$C
Fan number $C
The fans are no longer redundant due to fan
number $C failing
Error
F_$C
Fan number $C
The fans are no longer redundant due to fan
number $C failing
Error
F_$C
Fan number $C
The fans are no longer redundant due to fan
number $C failing
Error
F_$C
Fan number $C
The fans are no longer redundant due to fan
number $C failing
Error
Document # 1000000002666 v00
Item Name
Message
Status
F_$C
Fan number $C
The fans are no longer redundant due to fan
number $C failing
Error
F_$C
Fan number $C
The fans are redundant again
OK
TEMP
System Board
Temperature
The system board temperature has exceeded
the normal range
Error
TEMP
System Board
Temperature
The system board temperature is back within
normal range
OK
BMC_
FW
BMC Firmware
Health
The BMC board has detected a sensor failure
Error
F1
Fan 1
Fan number 1 is not functioning
Error
F1
Fan 1
Fan number 1 is functioning
OK
F2
Fan 2
Fan number 2 is not functioning
Error
F2
Fan 2
Fan number 2 is functioning
OK
F3
Fan 3
Fan number 3 is not functioning
Error
F3
Fan 3
Fan number 3 is functioning
OK
F4
Fan 4
Fan number 4 is not functioning
Error
F4
Fan 4
Fan number 4 is functioning
OK
F5
Fan 5
Fan number 5 is not functioning
Error
F5
Fan 5
Fan number 5 is functioning
OK
PS_$C
Power supply
number $C
The number $C AC power supply is no
longer available
Error
PS_$C
Power supply
number $C
The number $C AC power supply has been
connected
OK
PS_$C
Power supply
number $C
The number $C AC power supply has
recovered from failure
OK
PS_$C
Power supply
number $C
The number $C AC power supply has
detected a failure
Error
PS_$C
Power supply
number $C
The number $C AC power supply has
recovered from a predictive failure
OK
PS_$C
Power supply
number $C
The number $C AC power supply has
detected a predictive failure
Error
PS_$C
Power supply
number $C
The number $C AC power supply has been
lost
Error
PS_$C
Power supply
number $C
The number $C AC power supply has been
restored
OK
BaseSpace Onsite v1.0 LT System Guide
59
Admin Tasks
Error
Code/
Item
ID
Error
Code/
Item
ID
60
Item Name
Message
Status
PS_$C
Power supply
number $C
The number $C AC power supply has
resolved the configuration error for a vendor
mismatch
OK
PS_$C
Power supply
number $C
The number $C AC power supply has
detected a configuration error for a vendor
mismatch
Error
PS_$C
Power supply
number $C
The number $C AC power supply has
resolved the configuration error for a revision
mismatch
OK
PS_$C
Power supply
number $C
The number $C AC power supply has
detected a configuration error for a revision
mismatch
Error
PS_$C
Power supply
number $C
The number $C AC power supply has
resolved the configuration error for a missing
processor
OK
PS_$C
Power supply
number $C
The number $C AC power supply has
detected a configuration error for a missing
processor
Error
PS_$C
Power supply
number $C
The number $C AC power supply has
resolved an unexpected configuration error
OK
PS_$C
Power supply
number $C
The number $C AC power supply has
detected an unexpected configuration error
Error
CBPB
Chassis Back
Panel Board
The panel board in the back of the chassis has
changed to being offline
Error
CBPB
Chassis Back
Panel Board
The panel board in the back of the chassis is
back online
OK
P_$C
Processor
number $C
The processor number $C has exceeded the
normal range
Error
P_$C
Processor
number $C
The processor number $C is back within the
normal range
OK
P_$C
Processor
number $C
The processor number $C has been detected
OK
P_$C
Processor
number $C
The processor number $C is not being
detected
OK
P_ERR_
$C
Processor
number $C
digital state error
The processor number $C has detected a
digital state error
Error
P_ERR_
$C
Processor
number $C
digital state error
The processor number $C has recovered
from a digital state error
OK
Document # 1000000002666 v00
Item Name
Message
Status
P_
TEMP_
$C
System
temperature
The system temperature has exceeded its
threshold
Error
P_
TEMP_
$C
System
temperature
The system temperature is back within
normal operating range
OK
PS_
FAN_
$C
Power Supply
Fan $C
The power supply fan number $C has failed
Error
PS_
FAN_
$C
Power Supply
Fan $C
The power supply fan number $C has been
restored
OK
M_$C
Memory Sensor
number $C
The thermal sensor at memory location $C
has exceeded its threshold
Error
M_$C
Memory Sensor
number $C
The thermal sensor at memory location $C is
back within normal range
OK
HD_$C
Disk in slot $C
Disk rebuild in progress at slot $C
Error
HD_$C
Disk in slot $C
Disk rebuild at slot $C has completed
OK
HD_$C
Disk in slot $C
Disk at slot $C is no longer online
Error
HD_$C
Disk in slot $C
Disk at slot $C is back online
OK
HD_$C
Disk in slot $C
Disk at slot $C is no longer working
HD_$C
Disk in slot $C
Disk at slot $C is no functioning correctly
again
LV_$B
Logical volume
$B with capacity
$C $D
The logical volume at $B size $C $D is not
currently active
BaseSpace Onsite v1.0 LT System Guide
Admin Tasks
Error
Code/
Item
ID
Error
61
Notes
For technical assistance, contact Illumina Technical Support.
Table 2 Illumina General Contact Information
Website
Email
www.illumina.com
[email protected]
Table 3 Illumina Customer Support Telephone Numbers
Region
Contact Number
Region
North America
1.800.809.4566
Italy
Australia
1.800.775.688
Netherlands
Austria
0800.296575
New Zealand
Belgium
0800.81102
Norway
Denmark
80882346
Spain
Finland
0800.918363
Sweden
France
0800.911850
Switzerland
Germany
0800.180.8994
United Kingdom
Ireland
1.800.812949
Other countries
Contact Number
800.874909
0800.0223859
0800.451.650
800.16836
900.812168
020790181
0800.563118
0800.917.0041
+44.1799.534000
Safety data sheets (SDSs)—Available on the Illumina website at
support.illumina.com/sds.html.
Product documentation—Available for download in PDF from the Illumina website. Go
to support.illumina.com, select a product, then select Documentation & Literature.
BaseSpace Onsite v1.0 LT System Guide
Technical Assistance
Technical Assistance
Illumina
San Diego, California 92122 U.S.A.
+1.800.809.ILMN (4566)
+1.858.202.4566 (outside North America)
[email protected]
www.illumina.com
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