Closed StefanBabukov closed 5 months ago
Background Here a user reported an error in gem2s. Upon checking, the error was seurat's pipeline:
26 seurat-2-load_seurat.R#51: stop(errors$ERROR_SEURAT_RDS, call. = FALSE) 27 .handleSimpleError(function (c) { if (inherits(c, "condition") & ERROR [2023-08-02 11:22:35] 🚩 --------- R error at filter step processSeurat! : ERROR_SEURAT_RDS .... recovered from error:ERROR_SEURAT_RDS You can see the full log here. The issue is that the experiment parameters show that it's a normal experiment, not a seurat. Here's the relevant part of the pipeline parameters showing that the files are 10x format.
| 2023-08-02T13:22:35.013+02:00 | ..$ 277f0fd5-7f4d-4d0b-9f26-3c9cc9d5501e:List of 3 | 2023-08-02T13:22:35.013+02:00 | .. ..$ matrix10x : chr "cab3cda0-5631-417d-b299-b0ead7846be9" | 2023-08-02T13:22:35.014+02:00 | .. ..$ barcodes10x: chr "1067a8cd-5c8c-4987-87c3-be8e8b99c076" | 2023-08-02T13:22:35.015+02:00 | .. ..$ features10x: chr "08e44dfd-1c94-4357-a66f-50453bb5ed5c"
Todo Check why the seurat pipeline is being triggered.
Background Here a user reported an error in gem2s. Upon checking, the error was seurat's pipeline:
26 seurat-2-load_seurat.R#51: stop(errors$ERROR_SEURAT_RDS, call. = FALSE) 27 .handleSimpleError(function (c) { if (inherits(c, "condition") & ERROR [2023-08-02 11:22:35] 🚩 --------- R error at filter step processSeurat! : ERROR_SEURAT_RDS .... recovered from error:ERROR_SEURAT_RDS You can see the full log here. The issue is that the experiment parameters show that it's a normal experiment, not a seurat. Here's the relevant part of the pipeline parameters showing that the files are 10x format.
$ sampleS3Paths :List of 7
| 2023-08-02T13:22:35.013+02:00 | ..$ 277f0fd5-7f4d-4d0b-9f26-3c9cc9d5501e:List of 3 | 2023-08-02T13:22:35.013+02:00 | .. ..$ matrix10x : chr "cab3cda0-5631-417d-b299-b0ead7846be9" | 2023-08-02T13:22:35.014+02:00 | .. ..$ barcodes10x: chr "1067a8cd-5c8c-4987-87c3-be8e8b99c076" | 2023-08-02T13:22:35.015+02:00 | .. ..$ features10x: chr "08e44dfd-1c94-4357-a66f-50453bb5ed5c"
Todo Check why the seurat pipeline is being triggered.