Hi,
I connected to a loom file with connect function; added metadata using add.col.attribute and add.row.attribute. Then trying to subset a loom file with subset function, based on the added metadata. File is created, and opened, but after reaching 100% "adding data" getting an error.
m <- grep(pattern = "mm10", x = lfile[["col_attrs/call"]][], value = FALSE)
s <- grep(pattern = "mm10", x = lfile[["row_attrs/Gene"]][], value = FALSE)
loom_out <- subset(lfile,
m = m,
n = s,
filename = NULL, overwrite = T, display.progress = TRUE)
Writing new loom file to cellranger/S_combined_subset.loom
Adding data for /matrix and 3 layers
|=================================================================================================================================================| 100%
Error in new.loom$create_group(name = group) : HDF5-API Errors:
error #000: H5G.c in H5Gcreate2(): line 323: unable to create group
class: HDF5
major: Symbol table
minor: Unable to initialize object
error #001: H5Gint.c in H5G__create_named(): line 157: unable to create and link to group
class: HDF5
major: Symbol table
minor: Unable to initialize object
error #002: H5L.c in H5L_link_object(): line 1557: unable to create new link to object
class: HDF5
major: Links
minor: Unable to initialize object
error #003: H5L.c in H5L__create_real(): line 1798: can't insert link
class: HDF5
major: Links
minor: Unable to insert object
error #004: H5Gtraverse.c in H5G_traverse(): line 851: internal path traversal failed
class: HDF5
major: Symbol table
minor: Object not found
error #005: H5Gtraverse.c in H5G__traverse_real(): line 627: traversal operator failed
class: HDF5
ma
Any ideas what is causing this? I can't find any troubleshooting threads so far.
Thank you in advance,
Maria
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] loomR_0.2.1.9000 R6_2.4.0 data.table_1.12.6 Signac_0.1.5 hdf5r_1.3.0 ggplot2_3.2.1 Seurat_3.1.1