Question: Rsubread align() output_file, dir not created first
0
gravatar for Michael Love
3.5 years ago by
Michael Love22k
United States
Michael Love22k wrote:

hi,

I noticed, when I try to align() and give an output file path which includes a non-existent directory, I get a segfault instead of an error message. Here using development branch, and the example code from the vignette, but adding "foo/" to the output_file argument:

> library(Rsubread) 
> ref <- system.file("extdata","reference.fa",package="Rsubread")        
> buildindex(basename="reference_index",reference=ref)  
> reads <- system.file("extdata","reads.txt.gz",package="Rsubread")       
> align(index="reference_index",readfile1=reads,output_file="foo/alignResults.BAM")                 
                                                                                                     
         ==========     _____ _    _ ____  _____  ______          _____                              
         =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \                             
           =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |                            
             ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |                            
               ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |                            
         ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/                             
        Rsubread 1.19.3                                                                              
                                                                                                     
 //========================== subread-align setting ===========================\\                    
 ||                                                                            ||                    
 ||           Function : Read alignment                                        ||                    
 ||            Threads : 1                                                     ||                    
 ||         Input file : /home/love/bin/R/library/Rsubread/extdata/reads.t ... ||                    
 ||        Output file : foo/alignResults.BAM (BAM)                            ||                    
 ||         Index name : reference_index                                       ||                    
 ||       Phred offset : 33                                                    ||                    
 ||                                                                            ||                    
 ||          Min votes : 3                                                     ||                    
 ||         Max indels : 5                                                     ||                    
 ||  # of Best mapping : 1                                                     ||                    
 ||     Unique mapping : yes                                                   ||                    
 ||   Hamming distance : yes                                                   ||                    
 ||     Quality scores : no                                                    ||                    
 ||                                                                            ||                    
 \\===================== http://subread.sourceforge.net/ ======================//                    
                                                                                                     
 //====================== Running (11-Sep-2015 10:06:38) ======================\\                    
 ||                                                                            ||                    
 || Decompress /home/love/bin/R/library/Rsubread/extdata/reads.txt.gz...       ||                    
 || The input file contains base space reads.                                  ||                    
 || WARNING The specified phred-score offset (33) seems to be incorrect.       ||                    
 ||         The observed phred-score range is [66,98].                         ||                    
 ||                                                                            ||                    

                                                                                                     
  *** caught segfault ***                                                                            
 address 0x8, cause 'memory not mapped'                                                              
                                                                                                     
 Traceback:                                                                                          
  1: .C("R_align_wrapper", as.integer(n), as.character(cmd), PACKAGE = "Rsubread")                   
  2: align(index = "reference_index", readfile1 = reads, output_file = "foo/alignResults.BAM")       
                                                                                                     
 Possible actions:                                                                                   
 1: abort (with core dump, if enabled)                                                               
 2: normal R exit                                                                                    
 3: exit R without saving workspace                                                                  
 4: exit R saving workspace                                                                          
 Selection:              


> sessionInfo()                                                                                     
 R Under development (unstable) (2015-06-21 r68565)                                                  
 Platform: x86_64-unknown-linux-gnu (64-bit)                                                         
 Running under: Ubuntu 15.04                                                                         
                                                                                                     
 locale:                                                                                             
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8                      
  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8                  
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C                             
 [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C                      
                                                                                                     
 attached base packages:                                                                             
 [1] stats     graphics  grDevices datasets  utils     methods   base                                
                                                                                                     
 other attached packages:                                                                            
 [1] Rsubread_1.19.3                                                                                 
                                                                                                     
 loaded via a namespace (and not attached):                                                          
 [1] compiler_3.3.0 tools_3.3.0     

 

rsubread • 701 views
ADD COMMENTlink modified 3.5 years ago by Wei Shi3.0k • written 3.5 years ago by Michael Love22k
Answer: Rsubread align() output_file, dir not created first
1
gravatar for Wei Shi
3.5 years ago by
Wei Shi3.0k
Australia
Wei Shi3.0k wrote:

Hi Michael, thanks for reporting this problem. I have added new code to the function to check if the directory included in the output file name is valid. It will now report an error if the directory does not exist. Changes were just committed to svn devel repository and should be available to you in a couple of days.
 

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Wei Shi3.0k
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