The BUG appears to be caused when the NCBI environment variable is undefined. Setting NCBI to the installed location of the default config file under Ubuntu fixes the problem:
> ajt@beluga:~$ export NCBI=/etc/ncbi
> ajt@beluga:~$ strace blastn |& fgrep .ncbirc
> stat("./.ncbirc", 0x7ffc01d0e2c0) = -1 ENOENT (No such file or directory)
> stat("/home/ajt/.ncbirc", 0x7ffc01d0e2c0) = -1 ENOENT (No such file or directory)
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> lstat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
> openat(AT_FDCWD, "/etc/ncbi/.ncbirc", O_RDONLY) = 3
> stat("./.ncbirc", 0x7ffc01d0eae0) = -1 ENOENT (No such file or directory)
> stat("/home/ajt/.ncbirc", 0x7ffc01d0eae0) = -1 ENOENT (No such file or directory)
> stat("/etc/ncbi/.ncbirc", {st_mode=S_IFREG|0644, st_size=1229, ...}) = 0
This behaviour is consistent to what NCBI describe:
If the NCBI variable is unset, "blastn" looks for "/etc/.ncbirc". However, the default location the config file is installed to under Ubuntu is "/etc/ncbi/.ncbirc".
The BUG appears to be caused when the NCBI environment variable is undefined. Setting NCBI to the installed location of the default config file under Ubuntu fixes the problem:
> ajt@beluga:~$ export NCBI=/etc/ncbi home/ajt/ .ncbirc" , 0x7ffc01d0e2c0) = -1 ENOENT (No such file or directory) etc/ncbi/ .ncbirc" , {st_mode= S_IFREG| 0644, st_size=1229, ...}) = 0 etc/ncbi/ .ncbirc" , {st_mode= S_IFREG| 0644, st_size=1229, ...}) = 0 etc/ncbi/ .ncbirc" , {st_mode= S_IFREG| 0644, st_size=1229, ...}) = 0 /etc/ncbi/ .ncbirc" , {st_mode= S_IFREG| 0644, st_size=1229, ...}) = 0 .ncbirc" , O_RDONLY) = 3 home/ajt/ .ncbirc" , 0x7ffc01d0eae0) = -1 ENOENT (No such file or directory) etc/ncbi/ .ncbirc" , {st_mode= S_IFREG| 0644, st_size=1229, ...}) = 0
> ajt@beluga:~$ strace blastn |& fgrep .ncbirc
> stat("./.ncbirc", 0x7ffc01d0e2c0) = -1 ENOENT (No such file or directory)
> stat("/
> stat("/
> stat("/
> stat("/
> lstat("
> openat(AT_FDCWD, "/etc/ncbi/
> stat("./.ncbirc", 0x7ffc01d0eae0) = -1 ENOENT (No such file or directory)
> stat("/
> stat("/
This behaviour is consistent to what NCBI describe:
> https:/ /www.ncbi. nlm.nih. gov/books/ NBK279695/
If the NCBI variable is unset, "blastn" looks for "/etc/.ncbirc". However, the default location the config file is installed to under Ubuntu is "/etc/ncbi/ .ncbirc" .