HDF5-Diag issue

[ldudley7]

Hi all,

I am having an issue when attempting to run this line of the code: x.sp.ls = lapply(seq(snap.files), function(i){createSnap(file=snap.files[i], sample=sample.names[i]);})

I am getting this error message: Epoch: reading the barcode session ... HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:

000: H5Dio.c line 174 in H5Dread(): can't read data

major: Dataset
minor: Read failed

001: H5Dio.c line 448 in H5D_read(): can't read data

major: Dataset
minor: Read failed

002: H5Dchunk.c line 1729 in H5D_chunk_read(): unable to read raw data chunk

major: Low-level I/O
minor: Read failed

003: H5Dchunk.c line 2760 in H5D_chunk_lock(): data pipeline read failed

major: Data filters
minor: Filter operation failed

004: H5Z.c line 1094 in H5Z_pipeline(): required filter is not registered

major: Data filters
minor: Read failed

caught segfault address (nil), cause 'memory not mapped'

Traceback: 1: H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, compoundAsDataFrame = compoundAsDataFrame, drop = drop, ...) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 4: tryCatchList(expr, classes, parentenv, handlers) 5: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))}) 6: try({ obj <- H5Dread(h5dataset = h5dataset, h5spaceFile = h5spaceFile, h5spaceMem = h5spaceMem, compoundAsDataFrame = compoundAsDataFrame, drop = drop, ...)}) 7: h5readDataset(h5dataset, index = index, start = start, stride = stride, block = block, count = count, compoundAsDataFrame = compoundAsDataFrame, drop = drop, ...) 8: h5read(file, "/BD/name") 9: doTryCatch(return(expr), name, parentenv, handler) 10: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 11: tryCatchList(expr, classes, parentenv, handlers) 12: tryCatch(barcode <- h5read(file, "/BD/name"), error = function(e) { print(paste("Warning @readSnap: 'BD/name' not found in ", file)) return(vector(mode = "character", length = 0))}) 13: createSnapSingle(file = fileList[[i]], sample = sampleList[[i]]) 14: FUN(X[[i]], ...) 15: lapply(as.list(seq(fileList)), function(i) { createSnapSingle(file = fileList[[i]], sample = sampleList[[i]])}) 16: createSnap.default(file = snap.files[i], sample = sample.names[i]) 17: createSnap(file = snap.files[i], sample = sample.names[i]) 18: FUN(X[[i]], ...) 19: lapply(seq(snap.files), function(i) { createSnap(file = snap.files[i], sample = sample.names[i])})

Any help would be extremely appreciated. Please let me know if you need any system details to help further.