From 6f7b01d369c9212b9a2f015945005a54653b70de Mon Sep 17 00:00:00 2001
From: huidongchen <hd7chen@gmail.com>
Date: Fri, 8 Sep 2023 10:52:28 -0400
Subject: [PATCH] del unnecessary file

---
 stream2/preprocessing/stream2_chromVar.out | 78 ----------------------
 1 file changed, 78 deletions(-)
 delete mode 100644 stream2/preprocessing/stream2_chromVar.out

diff --git a/stream2/preprocessing/stream2_chromVar.out b/stream2/preprocessing/stream2_chromVar.out
deleted file mode 100644
index 7e241c5..0000000
--- a/stream2/preprocessing/stream2_chromVar.out
+++ /dev/null
@@ -1,78 +0,0 @@
-
-R version 4.1.3 (2022-03-10) -- "One Push-Up"
-Copyright (C) 2022 The R Foundation for Statistical Computing
-Platform: x86_64-conda-linux-gnu (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> suppressMessages(library(chromVAR))
-> suppressMessages(library(Matrix))
-> suppressMessages(library(SummarizedExperiment))
-> suppressMessages(library(BiocParallel))
-> suppressMessages(library(data.table))
-> 
-> set.seed(2022)
-> 
-> ### Get command line arguments
-> args <- commandArgs(TRUE)
-> print(args[[1]])
-[1] "input='.'"
-> print(args[[2]])
-[1] "species='MusMusculus'"
-> print(args[[3]])
-[1] "genome='mm10'"
-> print(args[[4]])
-[1] "feature='motif'"
-> print(args[[5]])
-[1] "n_jobs=4"
-> 
-> if(length(args)<5){
-+     print("Not sufficient arguments supplied.")
-+ }else{
-+     for(i in 1:length(args)){
-+       eval(parse(text=args[[i]]))
-+     }
-+ }
-> 
-> print(paste0('input is ', input))
-[1] "input is ."
-> print(paste0('species is ', species))
-[1] "species is MusMusculus"
-> print(paste0('genome is ', genome))
-[1] "genome is mm10"
-> print(paste0('feature is ', feature))
-[1] "feature is motif"
-> print(paste0('n_jobs is ', n_jobs))
-[1] "n_jobs is 4"
-> 
-> if(species=='HomoSapiens'){
-+     species = 'Homo sapiens'
-+ }else if(species=='MusMusculus'){
-+     species = 'Mus musculus'
-+ }else{
-+     print("Only 'HomoSapiens' and 'MusMusculus' are supported")
-+     break
-+ }
->     
-> print(paste0('Using',n_jobs,'cores...',sep = " "))
-[1] "Using4cores... "
-> register(MulticoreParam(n_jobs))
-> 
-> ### Read in data files
-> print(paste0('Read in regions: ', input, '/region_file.bed...'))
-[1] "Read in regions: ./region_file.bed..."
-> peaks <- makeGRangesFromDataFrame(data.frame(fread(paste0(input,'/region_file.bed'),col.names=c('seqnames','start','end'))))
-Error in fread(paste0(input, "/region_file.bed"), col.names = c("seqnames",  : 
-  File './region_file.bed' does not exist or is non-readable. getwd()=='/mnt/c/Users/jobac/Desktop/all/git/STREAM2/stream2/preprocessing'
-Calls: makeGRangesFromDataFrame -> data.frame -> fread
-Execution halted