On Wed, 31 Jul 2019 07:09:16 +0200 Andreas Tille <andr...@fam-tille.de>
wrote:
> Control: tags -1 help
>
> Hi,
>
> unfortunately I have no idea what to do to solve this
> except to exclude this architecture. Any hint would
> be more than welcome.
>
> Kind regards
>
> Andreas.
>
> --
> http://fam-tille.de
>
>
I have investigated more - the failing test is
bamtools filter -script tests/filter_script -in sam_spec_example.bam
-out out.bam
all other tests pass.
#----------------------------------------------------------------------------
which traced gives
execve("/usr/bin/bamtools", ["bamtools", "filter", "-script",
"tests/filter_script", "-in", "sam_spec_example.bam", "-out",
"out.bam"], 0x7fffd265a250 /* 14 vars */) = 0
fstat(3, {st_mode=S_IFREG|0644, st_size=198896, ...}) = 0
mmap(NULL, 262552, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0)
= 0x7fff97cd0000
mmap(0x7fff97d00000, 131072, PROT_READ|PROT_WRITE,
MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x20000) = 0x7fff97d00000
close(3) = 0
mprotect(0x7fff97f20000, 65536, PROT_READ) = 0
mprotect(0x7fff97d00000, 65536, PROT_READ) = 0
mprotect(0x7fff97f60000, 65536, PROT_READ) = 0
mprotect(0x7fff980a0000, 65536, PROT_READ) = 0
mprotect(0x7fff98320000, 65536, PROT_READ) = 0
mprotect(0x7fff983e0000, 65536, PROT_READ) = 0
mprotect(0x7fff98440000, 65536, PROT_READ) = 0
mprotect(0x12ce50000, 65536, PROT_READ) = 0
mprotect(0x7fff984f0000, 65536, PROT_READ) = 0
munmap(0x7fff98460000, 215211) = 0
brk(NULL) = 0x1001ccb0000
brk(0x1001cce0000) = 0x1001cce0000
openat(AT_FDCWD, "tests/filter_script", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=352, ...}) = 0
read(3, "{\n \"filters\" : \n [\n { \""..., 4096) = 352
read(3, "", 4096) = 0
read(3, "", 4096) = 0
read(3, "", 4096) = 0
read(3, "", 4096) = 0
read(3, "", 4096) = 0
read(3, "", 4096) = 0
... and that forever
I have changed the filter_script to add more lines of data, and trace
shows like at the end of file it doesn't get EOF and try to read more -
don't understand why !
openat(AT_FDCWD, "/tmp/filter_script", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=63521, ...}) = 0
read(3, "{\n \"filters\" : \n [\n { \""..., 4096) = 4096
read(3, " }\n{ "..., 4096) = 4096
read(3, " "..., 4096) = 4096
brk(0x100387e0000) = 0x100387e0000
read(3, " "..., 4096) = 4096
read(3, " "..., 4096) = 4096
read(3, " "..., 4096) = 2081
read(3, "", 4096) = 0
