Subscript out of bounds error during spatial integration in st_cluster.R #29
Description
Thank you for making such a great tool!
I encountered an error while running st_cluster.R from the STTKIT package. The script terminates with a subscript out-of-bounds error during the spatial integration step. Below are the details of the command used, the full log output, and relevant observations.
Warning messages:
1: Key ‘slice1_’ taken, using ‘bp1821023_’ instead
2: Key ‘slice1_’ taken, using ‘ah21171no29_’ instead
...
• These keys appear to be renamed automatically, but the process may not be working as intended.
Command:
Rscript $STTKIT/st_cluster.R
--infile '/home/ngs/Desktop/ipmn_sctransform.list'
--labels '/home/ngs/Desktop/ipmn_sctransform_labels.list'
--outprefix /media/ngs/SSD/STTKIT/cluster/ipmn
--gmt /home/ngs/Desktop/idep_cleaned.gmt
--extra_gmt /home/ngs/Downloads/c5.go.v2024.1.Hs.symbols.gmt
--min_features 200 --nmf --nmf_rank 4:16 --nmf_nruns 40
--nmf_randomize --nmf_method nsNMF --verbose
Log Output:
INFO [2025-01-10 18:33:48] Loading Seurat...
NULL
INFO [2025-01-10 18:33:54] Loading infiles A_P18_210_17_scaled.rds, B_P18_210_23_scaled.rds, A_H21-171_No29_scaled.rds, B_P19-927_No42_scaled.rds, 33_1_scaled.rds, 39_1_scaled.rds...
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Spatial
Updating slots in SCT
Updating slots in A_P18_210_17
Setting assay used for NormalizeData.Spatial to Spatial
Setting assay used for SCTransform.Spatial to Spatial
Validating object structure for Assay5 ‘Spatial’
Validating object structure for SCTAssay ‘SCT’
Validating object structure for VisiumV2 ‘A_P18_210_17’
Object representation is consistent with the most current Seurat version
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Spatial
Updating slots in SCT
Updating slots in B_P18_210_23
Setting assay used for NormalizeData.Spatial to Spatial
Setting assay used for SCTransform.Spatial to Spatial
Validating object structure for Assay5 ‘Spatial’
Validating object structure for SCTAssay ‘SCT’
Validating object structure for VisiumV2 ‘B_P18_210_23’
Object representation is consistent with the most current Seurat version
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Spatial
Updating slots in SCT
Updating slots in A_H21.171_No29
Setting assay used for NormalizeData.Spatial to Spatial
Setting assay used for SCTransform.Spatial to Spatial
Validating object structure for Assay5 ‘Spatial’
Validating object structure for SCTAssay ‘SCT’
Validating object structure for VisiumV2 ‘A_H21.171_No29’
Object representation is consistent with the most current Seurat version
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Spatial
Updating slots in SCT
Updating slots in B_P19.927_No42
Setting assay used for NormalizeData.Spatial to Spatial
Setting assay used for SCTransform.Spatial to Spatial
Validating object structure for Assay5 ‘Spatial’
Validating object structure for SCTAssay ‘SCT’
Validating object structure for VisiumV2 ‘B_P19.927_No42’
Object representation is consistent with the most current Seurat version
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Spatial
Updating slots in SCT
Updating slots in X33_1
Setting assay used for NormalizeData.Spatial to Spatial
Setting assay used for SCTransform.Spatial to Spatial
Validating object structure for Assay5 ‘Spatial’
Validating object structure for SCTAssay ‘SCT’
Validating object structure for VisiumV2 ‘X33_1’
Object representation is consistent with the most current Seurat version
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Spatial
Updating slots in SCT
Updating slots in X39_1
Setting assay used for NormalizeData.Spatial to Spatial
Setting assay used for SCTransform.Spatial to Spatial
Validating object structure for Assay5 ‘Spatial’
Validating object structure for SCTAssay ‘SCT’
Validating object structure for VisiumV2 ‘X39_1’
Object representation is consistent with the most current Seurat version
INFO [2025-01-10 18:35:14] Doing a simple initial merge of --infile
INFO [2025-01-10 18:41:41] Loading --gmt...
Warning messages:
1: Key ‘slice1_’ taken, using ‘bp1821023_’ instead
2: Key ‘slice1_’ taken, using ‘ah21171no29_’ instead
3: Key ‘slice1_’ taken, using ‘bp19927no42_’ instead
4: Key ‘slice1_’ taken, using ‘x331_’ instead
5: Key ‘slice1_’ taken, using ‘x391_’ instead
INFO [2025-01-10 18:41:41] Selecting 3000 integration features.
INFO [2025-01-10 18:42:34] Adding additional features provided in --gmt.
INFO [2025-01-10 18:43:27] Not scaling input files.
INFO [2025-01-10 18:43:30] Percent Mito: Removing 2 cells from reference library 39_1.
Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds
Calls: integrate_spatial ... LayerData -> LayerData.Assay -> [ -> [ -> .subscript.2ary
In addition: There were 22 warnings (use warnings() to see them)
Execution halted