normalizing est_counts Error in if (sum(filter_bool) == 0)

[heskad]

Hello, dear friends! Help me please, i dont understand why Sleuth output that result :(

sample_id <- dir(file.path("~/Desktop/xxxxx/kallisto_output" ))
sample_id

kal_dirs <- file.path("~/Desktop/xxxxx/kallisto_output", sample_id, "kallisto")
kal_dirs

s2c <- read.table(file.path("~/Desktop/xxxxx/metadata/meta(copy).tsv"),
header = TRUE, stringsAsFactors = FALSE, sep = " ")

---

meta(copy)
sample_id genotype_variation_s
M_u_Kidney_c ref
M_u_Kidney_1 isoform
M_u_Kidney_2 isoform
M_u_Kidney_3 isoform
M_u_Kidney_4 isoform

---

s2c <- dplyr::select(s2c, sample = sample_id, genotype_variation_s)
s2c <- dplyr::mutate(s2c, path = kal_dirs)

s2c$genotype_variation_s <- as.factor(s2c$genotype_variation_s)
s2c$genotype_variation_s <- relevel(s2c$genotype_variation_s, ref = "c-like")

so <- sleuth_prep(s2c, ~genotype_variation_s, extra_bootstrap_summary = TRUE,
read_bootstrap_tpm=TRUE)

---

reading in kallisto results
dropping unused factor levels
.....
normalizing est_counts
Error in if (sum(filter_bool) == 0) { :
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In check_num_cores(num_cores) :
It appears that you are running Sleuth from within Rstudio.
Because of concerns with forking processes from a GUI, 'num_cores' is being set to 1.
If you wish to take advantage of multiple cores, please consider running sleuth from the command line.