Cogent NGS Discovery Software notices
The issues described below for the Cogent NGS Discovery Software are ones that have been seen or reported. If you encounter other errors using CogentDS or are unable to resolve the problem using the suggestions below, please:
- Capture a screenshot of the error you see on the screen.
- Send the screenshot to Technical Support, along with a brief description of the issue.
Software issues FAQs
Error pop-up: Choose R installation when running RStudio
Problem description
A pop-up error screen is displaying the title "Choose R installation" with the message "RStudio requires an existing installation of R in order to work. Please select the version of R to use."
Figure 1. Error pop-up seen when RStudio is unable to find the R installation in Windows.
Cause
Either RStudio can't find the installation of R or R is not installed on the computer.
Fix
Please contact your IT specialist for additional assistance.
Error: (converted from warning) cannot remove prior installation of package
Problem description
An error like the following is seen either during installation or an upgrade of Cogent NGS Discovery Software (package name 'glue' is provided as an example only):
Figure 2. Example of an R-dependency package upgrade error message.
Cause
This is an issue within R.
Fix
The workaround is to manually install the package(s) throwing the error(s).
install.packages("<PACKAGENAME>")
where <PACKAGENAME> is replaced with the name of the package to be re-installed.
Example:
install.packages("glue")
Figure 3. Example of a manual installation of the problem R package as depicted in Figure 2. Note the package was successfully unpacked and no error message occurred after the manual install.
Re-run the install/upgrade and repeat as necessary until no additional error messages are seen.
Error in loadNamespace, namespace '<PACKAGENAME>' #.#.# is being loaded, but >= #.#.# is required
Problem description
An error like the following is seen either during installation or an upgrade of Cogent NGS Discovery Software (package name 'processx' is provided as an example only):
Figure 4. Example of an R-dependency package error during installation.
Cause
This is an issue within R.
Fix
The workaround is to manually install the package(s) throwing the error(s).
install.packages("<PACKAGENAME>")
where <PACKAGENAME> is replaced with the name of the package to be re-installed.
Example:
install.packages("processx")
Figure 5. Example of a manual installation of the problem R package as depicted in Figure 4. Note the package was successfully unpacked and no error message occurred after the manual install.
Re-run the install/upgrade and repeat as necessary until no additional error messages are seen.
Error: .onLoad failed in loadNamespace() for '<PACKAGENAME>'
Problem description
In some cases when upgrading an R package using the install.packages() command, it may encounter an error and display a message like the one below (package name 'backports' is provided as an example only):
Figure 6. Example of an R-dependency package error during installation.
Cause
This is an issue within R.
Fix
Uninstall the package using the following command:
remove.packages("<PACKAGENAME>")
where <PACKAGENAME> is replaced with the name of the package to be uninstalled.
Example:
remove.packages("backports")
Re-run the package install (install.packages("<PACKAGENAME>")) and repeat as necessary until no additional error messages are seen.
Error: $ operator is invalid for atomic vectors
Problem description
A message displaying the title "Warning" and the text "Error: $ operator is invalid for atomic vectors" is seen.
Figure 1. Error pop-up seen when there are no samples remaining after the QC filtering step.
Alternatively, you may see messages like the following on the console of RStudio:
"Post QC 0 Samples & 0 Genes. Please modify parameters and try again."
"error | too few samples / genes"
Figure 2. Error messages that might be seen on the RStudio console when there are no samples remaining after the QC filtering step.
Cause
The errors indicate no samples were retained after the QC filtering step. This scenario is usually due to a high percentage (fraction) of mitochondrial or intergenic reads.
Fix
-
Check the
stats.csvfile —each fraction can be calculated with the formulas in the table below:Value Formula % Intergenic Reads Intergenic_Reads (column 14)
Uniquely_Mapped_Reads (column 8)% Mitochondrial Reads Mitochondrial_Reads (column 16)
Uniquely_Mapped_Reads -
Change the threshold for the "Mitochondrial Fraction Threshold", "Intergenic Fraction Threshold", or both if necessary, to a higher value (move the respective slider to the right) that will capture the calculated reads percentage. The default threshold of mitochondrial reads is 0-0.2 (0-20%) and of intergenic reads is 0-0.1 (0-10%); increasing the slider value increases the filter leniency.
Refer to Section V.C, "Run Quality Control and Clustering Modules" and the Quality Control window QC filter options in the Cogent NGS DS User Manual for more information on where these settings can be changed.
RNA-seq
Cogent NGS Analysis Pipeline
Analyze RNA-seq data generated by select Takara Bio applications.
Cogent NGS Discovery Software
Visualize RNA-seq data in UMAP or t-SNE charts from the output of the Cogent NGS Analysis Pipeline.
SMART-Seq DE3 Demultiplexer
Demultiplex sequencing data from the SMART-Seq v4 3′ DE Kit into sorted read data files.
Takara Bio USA, Inc.
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