subset giving HDF5-API Errors

[mliiv]

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

[gbloeb]

@mliiv Any progress, I'm having the same issue?

[mliiv]

Hi @gbloeb

if I remember correctly, then I dropped the idea of filtering the loom file with loomR since no luck with really fixing the error. Instead, I prepared the seurat object and then saved as the loom file (i.e. made all filtering in seurat). Important to always close loom files, even when had error in writing, and try again. Even if you get the errors, the loom file might be functional, just try and read in with python and check. Also, you can add attributes to the loom file without re-saving the file (lfile$close_all() will be enough to save and close) with e.g. lfile$add.col.attribute.
Also, I suspect the error might have had smth to do with the hdf5 package so making sure the install is solid would also be useful.

Best,
Maria

[zamlerd]

Hello,

I am having an issue subsetting a publicly available loom dataset here - https://console.cloud.google.com/storage/browser/linnarsson-lab-human;tab=objects?authuser=0&pli=1&prefix=&forceOnObjectsSortingFiltering=false

when trying to subset out a certain cluster

library(dplyr)
library(hdf5r)
library(loomR)
loom <- connect(filename = "~/Downloads/adult_human_20221007.loom", mode = "r+", skip.validate = TRUE)
attr.df <- loom$get.attribute.df(MARGIN = 2, col.names = "CellID", row.names = "Gene")
subset(loom, m = attr.df$Clusters == "298", filename = 'CBL.loom', chunk.size = 1000, verbose = T, overwrite = T)

I get the below error

Writing new loom file to CBL.loom
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) :
HDF5-API Errors:
error #000: ../../src/hdf5-1.12.1/src/H5F.c in H5Fcreate(): line 532: unable to create file
class: HDF5
major: File accessibility
minor: Unable to open file

error #001: ../../src/hdf5-1.12.1/src/H5VLcallback.c in H5VL_file_create(): line 3282: file create failed
    class: HDF5
    major: Virtual Object Layer
    minor: Unable to create file

error #002: ../../src/hdf5-1.12.1/src/H5VLcallback.c in H5VL__file_create(): line 3248: file create failed
    class: HDF5
    major: Virtual Object Layer
    minor: Unable to create file

error #003: ../../src/hdf5-1.12.1/src/H5VLnative_file.c in H5VL__native_file_create(): line 63: unable to create file
    class: HDF5
    major: File accessibility
    minor: Unable to open file

error #004: ../../src/hdf5-1.12.1/src/H5Fint.c in H5F_open(): line 1858: unable to truncate a file which is already open
    class: HDF5
    major: File ac

I am able to see things in the loom dataset, the output of
attr.df %>% colnames

is
[1] "Age" "CellCycle" "CellID" "Chemistry" "Clusters"
[6] "Donor" "DoubletFinderFlag" "DoubletFinderScore" "MT_ratio" "NGenes"
[11] "ROIGroupCoarse" "ROIGroupFine" "Roi" "SampleID" "Subclusters"
[16] "Tissue" "TotalUMI" "unspliced_ratio"

Which I know to be correct based on viewing with HDFView

Any help is appreciated

[MikaQiao]

Any updates? I'm having the same issue