Resource requirements
In the tutorial for the standard analysis track we utilized scRNAbox to analyze a snRNAseq dataset comprising of 11 samples and 53,998 high quality nuclei. The following job configurations were used for the analysis:
| Step | THREADS_ARRAY | MEM_ARRAY | WALLTIME_ARRAY |
|---|---|---|---|
| Step2 | 4 | 40g | 00-05:00 |
| Step3 | 4 | 40g | 00-05:00 |
| Step4 | 4 | 40g | 00-05:00 |
| Step5 | 4 | 100g | 00-05:00 |
| Step6 | 4 | 100g | 00-05:00 |
| Step7 MarkerGSEA | 4 | 40g | 00-05:00 |
| Step7 KnownMarkers | 4 | 40g | 00-02:00 |
| Step7 ReferenceAnnotation | 4 | 200g | 00-12:00 |
| Step7 Annotate | 4 | 40g | 00-01:00 |
| Step8 AddMeta | 4 | 40g | 00-02:00 |
| Step8 RunDGE | 4 | 40g | 00-12:00 |
Users should use the above configurations as a reference to determine the required resource configurations for their own analyses.
Common error messages
Step 5
Error message:
Error: Cannot find 'Sample_ID' in this Seurat object
Solution:
This error occurs when users initiate the pipeline at Step 5 (without running Steps 1 to 4). The 'Sample_ID' column of the metadata defines the identities of the individual samples which are being merged or integrated. In the scRNAbox pipeline, the 'Sample_ID' metadata column is added in Step 4. Therefore, to avoid this issue users should initiate the pipeline at Step 4 in order to obtain the required information for Step 5. Otherwise, users
can manually add a 'Sample_ID' metadata column corresponding to their sample identities prior to initiating the pipeline at Step 5. The following code can be used to add meta data to the Seurat object:
Seu_object <- AddMetadata(Seu_object, Sample_ID)
# Seu_object: Seurat object to be used in Step 5 of scRNAbox
# Sample_ID: Dataframe with rownames corresponding to the rownames of the Seurat object metadata and a "Sample_ID" column defining the sample identities of each cell.
If the error persists please contact the development team.
Step 6
Error message:
Error in FindClusters.Seurat(seu_int, resolution = par_FindClusters_resolution) :
Provided graph.name not present in Seurat object
Calls:
Solution:
This error occurs in Step 6 when users incorrectly define the "par_skip_integration" parameter. If you did not perform integration in Step 5 and simply merged the samples, set "par_skip_integration" to "Yes". Otherwise, if you performed sample integration in Step 5, set "par_skip_integration" to "No". After adjusting the "par_skip_integration" parameter to accurately reflect the analysis, re-run step 6. If the error persists please contact the development team.