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[josegarciamanteiga]

Dears, The error in the title is thrown with this debugging after calling create_bugreport_from_seurat(cds)

Metadata:
  
tool: loupeR
tool_version: 1.1.0
os: CentOS Linux 7 (Core)
system: x86_64-conda-linux-gnu (64-bit)
language: R
language_version: 4.3.3
extra:
     loupeR_seurat_version: 5.0.3
     loupeR_seurat_object_version: 5.0.2
     loupeR_hdf5r_version: 1.3.10
     loupeR_hdf5_version: 1.14.3
  
Selections:
  
selected assay:
    RNA
selected clusters:
    active_cluster
    orig.ident
    Phase
    old.ident
    RNA_snn_res.0.5
    seurat_clusters
    RNA_snn_res.0.6
    RNA_snn_res.1
    cell.type
    cell.supertype
    RNA_snn_res.1.2
    RNA_snn_res.1.5
    integrated_snn_res.0.5
    integrated_snn_res.0.7
    integrated_snn_res.1
    cell.type2
    pleura.types1
    cell_clusters_ok
    orig.ident_cell_clusters_ok
selected projections:
    umap
  
Matrix Sampling:
  
feature count: 18722
barcode count: 1075
feature sampling:
    SNUPN
    KRT5
    AL355802.2
    CRIPT
    SLC25A13
    SERTAD2
    ANG
    NT5DC3
    CHST13
    TSSC4
barcode sampling:
CAATACGGTTGCTCGG_1
    TACACGATCTGCCAGG_1
    CGCGGTATCCAAACTG_1
    ACGCCGAGTCTCCCTA_1
    ACAGCCGAGTGCGTGA_1
    GGATGTTGTTACGCCG_1
    ACCCACTTCAAAGTAG_1
    ATGGGAGGTACACCGC_1
    CGATCGGCAGATAATG_1
    CTTTCAAGTGAGTAAT_1
  
Validation:
  
    count matrix: (VALID)
    clusters:     (VALID)
    projections:  (VALID)

cds@version [1] ‘5.0.2’

While for another object no error is thrown with this debug: (which looks pretty similar to me...)

Metadata:
  
tool: loupeR
tool_version: 1.1.0
os: CentOS Linux 7 (Core)
system: x86_64-conda-linux-gnu (64-bit)
language: R
language_version: 4.3.3
extra:
     loupeR_seurat_version: 5.0.3
     loupeR_seurat_object_version: 5.0.2
     loupeR_hdf5r_version: 1.3.10
     loupeR_hdf5_version: 1.14.3
  
Selections:
  
selected assay:
    RNA
selected clusters:
    active_cluster
    orig.ident
    Phase
    old.ident
    RNA_snn_res.1
    seurat_clusters
    RNA_snn_res.0.5
    RNA_snn_res.0.4
    cell.type
    cell.supertype
    RNA_snn_res.0.1
    RNA_snn_res.0.2
    RNA_snn_res.0.3
    RNA_snn_res.0.6
    RNA_snn_res.0.7
    RNA_snn_res.0.8
    RNA_snn_res.0.9
    RNA_snn_res.1.2
    RNA_snn_res.1.1
    RNA_snn_res.0.95
    RNA_snn_res.0.99
    RNA_snn_res.1.5
    RNA_snn_res.0.15
    integrated_snn_res.0.5
    integrated_snn_res.0.1
    integrated_snn_res.0.09
    cell.clusters
selected projections:
    umap
  
Matrix Sampling:
feature count: 18758
barcode count: 8005
feature sampling:
    UBL4A
    MEGF8
    APPL2
    ADIPOR2
    NGFRAP1
    PLEK
    XYLB
    FAM91A1
    ZNHIT1
    IL1A
barcode sampling:
    CGCGTTTGTGTCCTCT_1
    TCGTACCAGGATATAC_5
    TGCACCTTCACCCGAG_5
    AGGGATGCAACTGCTA_5
    GATGAGGTCAATAAGG_5
    TGAGAGGTCACTCTTA_5
    CACATTTTCCTCCTAG_5
    GCTTCCATCTAACGGT_3
    TCAGCAAAGATCACGG_5
    TTCTACAGTGAGGGTT_1
  
Validation:
  
    count matrix: (VALID)
    clusters:     (VALID)
    projections:  (VALID)
> cds2@version
[1] ‘5.0.2’

Why is that? Thanks

sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
  
Matrix products: default
BLAS/LAPACK: /home/garciamanteiga.jose/.conda/envs/sceasy/lib/libopenblasp-r0.3.27.so;  LAPACK version 3.12.0
  
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
  
time zone: Europe/Rome
tzcode source: system (glibc)
  
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
  
other attached packages:
[1] Seurat_5.0.3       SeuratObject_5.0.2 sp_2.1-4           loupeR_1.1.0