rcorces
commented
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ehoreth
When I run the addIterativeLSI with my data the error message was appeared.
2023-09-18 10:32:02 : Computing Estimated LSI (projectAll = FALSE), 0.358 mins elapsed.
2023-09-18 10:32:24 : ERROR Found in .computeLSI for
LogFile = ArchRLogs/ArchR-addIterativeLSI-20ac173b0f63a6-Date-2023-09-18_Time-10-31-40.log
<subscriptOutOfBoundsError in allLSI[cn, , drop = FALSE]: subscript out of bounds>
2023-09-18 10:32:24 : ERROR Found in .LSIPartialMatrix for
LogFile = ArchRLogs/ArchR-addIterativeLSI-20ac173b0f63a6-Date-2023-09-18_Time-10-31-40.log
<simpleError in .logError(e, fn = ".computeLSI", info = "", errorList = errorList, logFile = logFile): Exiting See Error Above>
Error in .logError(e, fn = ".LSIPartialMatrix", info = "", errorList = errorList, : Exiting See Error Above In addition: Warning messages: 1: In h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles. 2: In h5checktypeOrOpenLoc(file, readonly = TRUE, fapl = NULL, native = native) : An open HDF5 file handle exists. If the file has changed on disk meanwhile, the function may not work properly. Run 'h5closeAll()' to close all open HDF5 object handles.
Here is my ruinnig code
total_proj_F2_T0_2 <- addIterativeLSI(ArchRProj = total_proj_F2_T0_1, useMatrix = "TileMatrix", name = "IterativeLSI", iterations = 2, clusterParams = list(resolution = c(0.01, 0.05, 0.1, 0.2, 0.4, 0.8), sampleCells = 1000, n.start = 5), varFeatures = 25000, threads = 1, dimsToUse = 1:30)
I changed the resolution for c(0.2), c(0.2, 0.3, 0.5), c(0.1) ... and aslo the sampleCells, n.start, varFeatures, dimToUse variables were changed some values But all results were failed and same error message was appeared.
I attempted my log.
Please help me
ArchR-addIterativeLSI-20ac17552555f5-Date-2023-09-15_Time-19-51-44.log