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Hello!
I am going though the vignette for DropletUtils and I am having an issue importing the the moleculeinfo.h5 file and I was wondering if it was because it was generated from a newer version of Cell Ranger (3.0.2) or if I need to patch and of my HDF5 software. the moleculeinfo.h5 file can be viewed with h5dump from the terminal. Here is my error message:
> mol.info <- read10xMolInfo('/data/met/Hong/02Apr19/S11M/molecule_info.h5')
HDF5-DIAG: Error detected in HDF5 (1.10.3) thread 0:
#000: H5D.c line 292 in H5Dopen2(): unable to open dataset
major: Dataset
minor: Can't open object
#001: H5Dint.c line 1205 in H5D__open_name(): not found
major: Dataset
minor: Object not found
#002: H5Gloc.c line 422 in H5G_loc_find(): can't find object
major: Symbol table
minor: Object not found
#003: H5Gtraverse.c line 851 in H5G_traverse(): internal path traversal failed
major: Symbol table
minor: Object not found
#004: H5Gtraverse.c line 627 in H5G__traverse_real(): traversal operator failed
major: Symbol table
minor: Callback failed
#005: H5Gloc.c line 378 in H5G__loc_find_cb(): object 'barcode' doesn't exist
major: Symbol table
minor: Object not found
Error in read10xMolInfo("/data/met/Hong/02Apr19/S11M/molecule_info.h5") :
c++ exception (unknown reason)
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.0
Matrix products: default
BLAS/LAPACK: /usr/local/lib/maths/atlas/ATLAS3.10.3/build/lib/libtatlas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] DropletUtils_1.2.2 SingleCellExperiment_1.4.1
[3] SummarizedExperiment_1.12.0 DelayedArray_0.8.0
[5] matrixStats_0.54.0 Biobase_2.42.0
[7] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[9] IRanges_2.16.0 S4Vectors_0.20.1
[11] BiocGenerics_0.28.0 BiocParallel_1.16.6
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 edgeR_3.24.3 XVector_0.22.0
[4] zlibbioc_1.28.0 lattice_0.20-38 tools_3.5.2
[7] grid_3.5.2 rhdf5_2.26.2 HDF5Array_1.10.1
[10] Matrix_1.2-17 GenomeInfoDbData_1.2.0 Rhdf5lib_1.4.3
[13] bitops_1.0-6 RCurl_1.95-4.12 limma_3.38.3
[16] compiler_3.5.2 locfit_1.5-9.1
Any advice or assistance is always greatly appreciated. Thank you!
Hello! I just saw in a previous answer that I will have to use the development version of DropletUtils with the CellRanger 3.0.2 output.
Hello!
I am using the development version of DropletUtils and It is loading the data, but now I am getting a segfault with the downsampling. It is only using one core for the downsampling even though it uses the BiocParallel library. Here is my error:
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