infercnv_obj = CreateInfercnvObject(raw_counts_matrix=counts_matrix,
annotations_file="annotation2.tab",
delim="\t",
gene_order_file="hg38_gencode_v27.txt",
ref_group_names= unique ( annt[grepl ( "Normal", annt$V2), ]$V2 ),
max_cells_per_group = 1200 # downsampling - may be set 1K
)
infercnv_obj2 = infercnv::run(infercnv_obj,
cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
out_dir=out_dir,
cluster_by_groups=TRUE,
denoise=TRUE,
cluster_references = F,
HMM=TRUE
, num_threads = 15
)
the above runs fine to completion, however when I set max_cells_per_group = to something like 5000 I get the error below.
I even try reducing the num_threads but results in the same error. Its not memory bc I'm only using half of what is available.
STEP 18: Run Bayesian Network Model on HMM predicted CNVs
INFO [2023-08-23 21:37:11] Initializing new MCM InferCNV Object.
INFO [2023-08-23 21:37:11] validating infercnv_obj
INFO [2023-08-23 21:37:12] Total CNV's: 476
INFO [2023-08-23 21:37:12] Loading BUGS Model.
INFO [2023-08-23 21:37:15] Running Sampling Using Parallel with 10 Cores
INFO [2023-08-24 11:00:27] Obtaining probabilities post-sampling
Error in do.call(rbind, mcmc[[j]]) : second argument must be a list
In addition: Warning message:
In parallel::mclapply(seq_along(obj@cell_gene), FUN = par_func, :
scheduled core 10 did not deliver a result, all values of the job will be affected
Hi my command is a follow
the above runs fine to completion, however when I set max_cells_per_group = to something like 5000 I get the error below. I even try reducing the num_threads but results in the same error. Its not memory bc I'm only using half of what is available.
verion: infercnv_1.10.1
thanks in advance!