I am running inferCNV on hg38 10x single-cell data. I am getting the following error when I try to execute the command. I inspected the gene order file and there don't seem to be any duplicates. Can you please help me with this?
I tried with pre-generated files from TrinityCTAT and also created it manually using gtf_to_position_file.py. I am getting this error anyway (Attaching the file here for reference).
Thank you very much!
Error:
INFO [2022-08-03 16:11:01] Parsing matrix: D6_counts_2.txt
INFO [2022-08-03 16:12:56] Parsing gene order file: gencode_v21_2.txt
Error in read.table(gene_order_file, header = FALSE, row.names = 1, sep = "\t", :
duplicate 'row.names' are not allowed
Calls: CreateInfercnvObject -> read.table
4: (function ()
traceback(2))()
3: stop("duplicate 'row.names' are not allowed")
2: read.table(gene_order_file, header = FALSE, row.names = 1, sep = "\t",
check.names = FALSE)
1: CreateInfercnvObject(raw_counts_matrix = "D6_counts_2.txt", annotations_file = "D6singleRannotation_encode.txt",
delim = "\t", gene_order_file = "gencode_v21_2.txt", ref_group_names = c("Monocytes"))
INFO [2022-08-03 16:12:56] ::process_data:Start
Error in infercnv::run(infercnv_obj, cutoff = 0.1, out_dir = out_dir, :
no slot of name "options" for this object of class "infercnv"
2: (function ()
traceback(2))()
1: infercnv::run(infercnv_obj, cutoff = 0.1, out_dir = out_dir,
cluster_by_groups = TRUE, analysis_mode = "subclusters",
plot_steps = FALSE, denoise = TRUE, sd_amplifier = 2, HMM = TRUE)
Hi,
I am running inferCNV on hg38 10x single-cell data. I am getting the following error when I try to execute the command. I inspected the gene order file and there don't seem to be any duplicates. Can you please help me with this?
I tried with pre-generated files from TrinityCTAT and also created it manually using gtf_to_position_file.py. I am getting this error anyway (Attaching the file here for reference).
Thank you very much!
Error:
INFO [2022-08-03 16:11:01] Parsing matrix: D6_counts_2.txt INFO [2022-08-03 16:12:56] Parsing gene order file: gencode_v21_2.txt Error in read.table(gene_order_file, header = FALSE, row.names = 1, sep = "\t", : duplicate 'row.names' are not allowed Calls: CreateInfercnvObject -> read.table 4: (function () traceback(2))() 3: stop("duplicate 'row.names' are not allowed") 2: read.table(gene_order_file, header = FALSE, row.names = 1, sep = "\t", check.names = FALSE) 1: CreateInfercnvObject(raw_counts_matrix = "D6_counts_2.txt", annotations_file = "D6singleRannotation_encode.txt", delim = "\t", gene_order_file = "gencode_v21_2.txt", ref_group_names = c("Monocytes")) INFO [2022-08-03 16:12:56] ::process_data:Start Error in infercnv::run(infercnv_obj, cutoff = 0.1, out_dir = out_dir, : no slot of name "options" for this object of class "infercnv" 2: (function () traceback(2))() 1: infercnv::run(infercnv_obj, cutoff = 0.1, out_dir = out_dir, cluster_by_groups = TRUE, analysis_mode = "subclusters", plot_steps = FALSE, denoise = TRUE, sd_amplifier = 2, HMM = TRUE)
gencode_v21_2.txt your_gen_pos.txt