bioconductor updated yet neoflow keeps showing update error #6
Description
I have been trying the 2. Variant peptide identification step with my own data and I keep getting the error that bioconductor is not updated which I already have along with R.
When I check R, it runs in the version of R version 4.2.1 (2022-06-23) and Bioconductor is in the version of 3.15.
> library(BiocManager)
Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
The error occurs in the last process and there were no issues during the example file run:
Below, I have attached the full error message once the command was executed:
[69/78f93c] process > msms_searching (PDAC_102076... [100%] 24 of 24, cached:...
[5c/bcddea] process > calculate_fdr (calculate_fdr) [100%] 1 of 1, cached: 1 ✔
[c8/3a5f19] process > prepare_pepquery_input (prep... [100%] 1 of 1, cached: 1 ✔
[55/8df182] process > run_pepquery (run_pepquery) [100%] 1 of 1, cached: 1 ✔
[55/4a2849] process > add_pepquery_validation (add... [100%] 1 of 1, failed: 1 ✘
Error executing process > 'add_pepquery_validation (add_pepquery_validation)'
Caused by:
Process add_pepquery_validation (add_pepquery_validation) terminated with an error exit status (1)
Command executed:
#!/usr/bin/env /usr/local/bin/Rscript
library(dplyr)
library(readr)
library(stringr)
psms <- read_tsv("novel_peptides_psm.tsv")
psm_rank_file = "pepquery/psm_rank.txt"
if(file.exists(psm_rank_file)){
psm_rank <- read_tsv(psm_rank_file)
if("n_ptm" %in% names(psm_rank)){
psm_rank <- psm_rank %>% filter(pvalue<=0.01,n_ptm==0,rank==1)
psms$pepquery <- ifelse(psms$peptide %in% psm_rank$peptide,1,0)
}else{
psms$pepquery <- 0
}
}else{
psms$pepquery <- 0
}
psms %>% write_tsv("novel_peptides_psm_pepquery.tsv")
Command exit status:
1
Command output:
(empty)
Command error:
Bioconductor version 3.10 (BiocManager 1.30.10), ?BiocManager::install for help
Bioconductor version '3.10' is out-of-date; the current release version '3.15'
is available with R version '4.2'; see https://bioconductor.org/install
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Parsed with column specification:
cols(
index = col_character(),
evalue = col_character(),
ion_score = col_character(),
charge = col_character(),
mass = col_character(),
mz = col_character(),
delta_da = col_character(),
delta_ppm = col_character(),
peptide = col_character(),
isdecoy = col_character(),
miss = col_character(),
protein = col_character(),
position = col_character(),
rt = col_character(),
isSAP = col_character(),
mods = col_character(),
FDR = col_character(),
Qvalue = col_character(),
is_novel = col_character()
)
Error in $<-.data.frame(*tmp*, pepquery, value = 0) :
replacement has 1 row, data has 0
Calls:
Execution halted
Would there be anything I may be missing?
Thank you again in advance