Error in density.default(dist_all, from = 0, to = dist_thre, n = dist_thre + : argument 'x' must be numeric

[kjHuoo]

Hi Vivian,
I got an error while using the offered example data to run the package, the same problem with Onur's.

Thank you,
Huoo

Code:

library(MAAPER) 
pas_anno <- readRDS('./mouse.PAS.mm9.rds')
gtf <- "./gencode.mm9.chr19.gtf"
bam_c1 <- "./NT_chr19_example.bam"
bam_c2 <- "./AS_4h_chr19_example.bam"
maaper(gtf, pas_anno, output_dir = "./",
       bam_c1, bam_c2,
       read_len = 76, ncores = 12)

Error:

Start training for condition c1 - sample 1 ...
86 genes used for training ...
1 fragments longer than 600 ...
Error in density.default(dist_all, from = 0, to = dist_thre, n = dist_thre +  : 
  argument 'x' must be numeric
Calls: maaper ... FUN -> get_pdist_singlePAS -> density -> density.default
In addition: Warning messages:
1: In dir.create(output_dir, recursive = T) : '.' already exists
2: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
3: In mclapply(1:length(pas_by_gene_single), function(i) { :
  all scheduled cores encountered errors in user code
Execution halted