@@ -21,7 +21,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

             params <- initialize(params, ...)

             params_list <- as.list(params)

             if (gsnap_split_output(params)) {

-              params_list$split_output <- output

+              params_list$split_output <- basename(output)

               output_path <- output_dir

             } else {

               output_path <- paste0(output, ".sam")

@@ -124,8 +124,10 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),

 }

 .system_gsnap <- function(command) {

-  command <- paste(command, "2>&1")

-  output <- .system(command, intern = TRUE)

+  stderr <- tempfile("gsnap-stderr", fileext = "log")

+  command <- paste(command, "2>", stderr)

+  .system(command)

+  output <- readLines(stderr)

   if (!gsnapSucceeded(command, output))

     stop("Execution of gsnap failed, command-line: '", command,

          "'; last output line: '", tail(output, 1), "'")