daisybio / daisybio/ASimulatoR
Error in endsWith(names(all_variants_and_event_annotation), "event_annotation")
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Description
I am trying to generate AS data.
I am using Homo_sapiens.GRCh38.115.gtf downloaded from https://ftp.ensembl.org/pub/release-115/gtf/homo_sapiens/
Here is the code i have used
```
suppressMessages(library(ASimulatoR))
input_dir = "/Fungel/abhilash/abhilash_home/genome_GTF/genome/ensemble"
num_reps = c(4,4)
outdir = 'simulation_nov'
max_genes = 3000
probs_as_freq = T
event_freq = setNames(rep(1/9, 9), c('es', 'mes', 'ir', 'a3', 'a5', 'afe', 'ale', 'mee', 'es,ir,mes,a3,a5,afe,ale,mee'))
simulate_alternative_splicing(input_dir = input_dir,
outdir = outdir,
event_probs = event_freq,
probs_as_freq = probs_as_freq,
max_genes = max_genes,
num_reps = num_reps,
ncores = 120,
seq_depth = 4e07,
verbose = TRUE)
```
The output is
```
found the following fasta files: 10.fa, 11.fa, 12.fa, 13.fa, 14.fa, 15.fa, 16.fa, 17.fa, 18.fa, 19.fa, 1.fa, 20.fa, 21.fa, 22.fa, 2.fa, 3.fa, 4.fa, 5.fa, 6.fa, 7.fa, 8.fa, 9.fa, MT.fa, X.fa, Y.fa
note that splice variants will only be constructed from chromosomes that have a corresponding fasta file
set data.table threads to 120
importing gtf/gff...
finished importing gtf/gff
creating superset...
|=============================================================================| 100%, Elapsed 00:28
finished creating superset
saving superset...
finished saving superset
assign variants to supersets...
create splicing variants and annotation. This may take a while...
| | 0%, ETA NA
Error in endsWith(names(all_variants_and_event_annotation), "event_annotation") :
non-character object(s)
In addition: Warning message:
In mclapply(X, function(...) { :
all scheduled cores encountered errors in user code
```
need some help in resolving this issue.
Thanks in advance
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