Strace

http://linux.die.net/man/1/strace

it's very interesting to use strace to trace all system calls in a process.
If you have strange error messages such as "permission denied" without further details, strace will allow you to get more info on what exactly was being executed at the time the error occurred.

In this example, here is what is run when zipping a file

orauser@ubuntu:/tmp$ echo ciao > ciao.txt
orauser@ubuntu:/tmp$ strace zip ciao.zip ciao.txt

execve("/usr/bin/zip", ["zip", "ciao.zip", "ciao.txt"], [/* 41 vars */]) = 0
brk(0) = 0x8f37000
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
mmap2(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb777a000
access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)
open("/etc/ld.so.cache", O_RDONLY) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=55536, ...}) = 0
mmap2(NULL, 55536, PROT_READ, MAP_PRIVATE, 3, 0) = 0xb776c000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
open("/lib/libbz2.so.1.0", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\0\20\0\0004\0\0\0"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0644, st_size=70036, ...}) = 0
mmap2(NULL, 68840, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xc6c000
mmap2(0xc7b000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0xf) = 0xc7b000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
open("/lib/i386-linux-gnu/libc.so.6", O_RDONLY) = 3
read(3, "\177ELF\1\1\1\0\0\0\0\0\0\0\0\0\3\0\3\0\1\0\0\0\220o\1\0004\0\0\0"..., 512) = 512
fstat64(3, {st_mode=S_IFREG|0755, st_size=1434180, ...}) = 0
mmap2(NULL, 1444360, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x5f5000
mprotect(0x74f000, 4096, PROT_NONE) = 0
mmap2(0x750000, 12288, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x15a) = 0x750000
mmap2(0x753000, 10760, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x753000
close(3) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb776b000
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb776a000
set_thread_area({entry_number:-1 -> 6, base_addr:0xb776bb40, limit:1048575, seg_32bit:1, contents:0, read_exec_only:0, limit_in_pages:1, seg_not_present:0, useable:1}) = 0
mprotect(0x750000, 8192, PROT_READ) = 0
mprotect(0xc7b000, 4096, PROT_READ) = 0
mprotect(0x8073000, 4096, PROT_READ) = 0
mprotect(0x949000, 4096, PROT_READ) = 0
munmap(0xb776c000, 55536) = 0
brk(0) = 0x8f37000
brk(0x8f58000) = 0x8f58000
open("/usr/lib/locale/locale-archive", O_RDONLY|O_LARGEFILE) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=8322432, ...}) = 0
mmap2(NULL, 2097152, PROT_READ, MAP_PRIVATE, 3, 0) = 0xb756a000
mmap2(NULL, 4096, PROT_READ, MAP_PRIVATE, 3, 0x2a1) = 0xb7779000
close(3) = 0
open("/etc/localtime", O_RDONLY) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=2819, ...}) = 0
fstat64(3, {st_mode=S_IFREG|0644, st_size=2819, ...}) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb7778000
read(3, "TZif2\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\4\0\0\0\4\0\0\0\0"..., 4096) = 2819
_llseek(3, -24, [2795], SEEK_CUR) = 0
read(3, "\nPST8PDT,M3.2.0,M11.1.0\n", 4096) = 24
close(3) = 0
munmap(0xb7778000, 4096) = 0
rt_sigaction(SIGINT, {0x804ab90, [INT], SA_RESTART}, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGTERM, {0x804ab90, [TERM], SA_RESTART}, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGABRT, {0x804ab90, [ABRT], SA_RESTART}, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGBUS, {0x804ab90, [BUS], SA_RESTART}, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGILL, {0x804ab90, [ILL], SA_RESTART}, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGSEGV, {0x804ab90, [SEGV], SA_RESTART}, {SIG_DFL, [], 0}, 8) = 0
open("ciao.zip", O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file or directory)
stat64("ciao.txt", {st_mode=S_IFREG|0644, st_size=5, ...}) = 0
time(NULL) = 1316294578
stat64("ciao.zip", 0x8076c40) = -1 ENOENT (No such file or directory)
open("/usr/lib/i386-linux-gnu/gconv/gconv-modules.cache", O_RDONLY) = -1 ENOENT (No such file or directory)
open("/usr/lib/i386-linux-gnu/gconv/gconv-modules", O_RDONLY) = 3
fstat64(3, {st_mode=S_IFREG|0644, st_size=55868, ...}) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb7778000
read(3, "# GNU libc iconv configuration.\n"..., 4096) = 4096
read(3, "B1.002//\nalias\tJS//\t\t\tJUS_I.B1.0"..., 4096) = 4096
read(3, "59-3\t1\nmodule\tINTERNAL\t\tISO-8859"..., 4096) = 4096
read(3, "859-14//\nalias\tISO-IR-199//\t\tISO"..., 4096) = 4096
read(3, "CDIC-DK-NO-A//\tEBCDIC-DK-NO-A\t1\n"..., 4096) = 4096
read(3, "\t\tIBM281//\t\tIBM281\t\t1\n\n#\tfrom\t\t\t"..., 4096) = 4096
read(3, "\tIBM863\t\t1\n\n#\tfrom\t\t\tto\t\t\tmodule"..., 4096) = 4096
read(3, "\tmodule\t\tcost\nalias\tIBM-939//\t\tI"..., 4096) = 4096
read(3, "\t\t\tmodule\t\tcost\nalias\tEUCCN//\t\t\t"..., 4096) = 4096
read(3, "C_P27-1//\t\tINTERNAL\t\tIEC_P27-1\t1"..., 4096) = 4096
read(3, "\t\t\tmodule\t\tcost\nalias\tMACIS//\t\t\t"..., 4096) = 4096
read(3, "X0213\t1\nmodule\tINTERNAL\t\tShift_J"..., 4096) = 4096
read(3, "40//\t\tIBM1140//\nalias\tCP1140//\t\t"..., 4096) = 4096
read(3, "\nmodule\tINTERNAL\t\tIBM16804//\t\tIB"..., 4096) = 2620
read(3, "", 4096) = 0
close(3) = 0
munmap(0xb7778000, 4096) = 0
time(NULL) = 1316294578
stat64("ciao.txt", {st_mode=S_IFREG|0644, st_size=5, ...}) = 0
stat64("/etc/localtime", {st_mode=S_IFREG|0644, st_size=2819, ...}) = 0
open("ciao.zip", O_WRONLY|O_CREAT|O_TRUNC|O_LARGEFILE, 0666) = 3
close(3) = 0
stat64("ciao.zip", {st_mode=S_IFREG|0644, st_size=0, ...}) = 0
unlink("ciao.zip") = 0
gettimeofday({1316294578, 909680}, NULL) = 0
getpid() = 6145
open("zijnRHbC", O_RDWR|O_CREAT|O_EXCL|O_LARGEFILE, 0600) = 3
fcntl64(3, F_GETFL) = 0x8002 (flags O_RDWR|O_LARGEFILE)
fstat64(3, {st_mode=S_IFREG|0600, st_size=0, ...}) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb7778000
_llseek(3, 0, [0], SEEK_CUR) = 0
munmap(0xb7778000, 4096) = 0
_llseek(3, 0, [0], SEEK_CUR) = 0
_llseek(3, 0, [0], SEEK_SET) = 0
fstat64(1, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 1), ...}) = 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xb7778000
write(1, " adding: ciao.txt", 18 adding: ciao.txt) = 18
stat64("ciao.txt", {st_mode=S_IFREG|0644, st_size=5, ...}) = 0
stat64("/etc/localtime", {st_mode=S_IFREG|0644, st_size=2819, ...}) = 0
stat64("ciao.txt", {st_mode=S_IFREG|0644, st_size=5, ...}) = 0
open("ciao.txt", O_RDONLY|O_LARGEFILE) = 4
write(3, "PK\3\4\24\0\10\0\10\0\321r1?\0\0\0\0\0\0\0\0\5\0\0\0\10\0\34\0ci"..., 66) = 66
read(4, "ciao\n", 65536) = 5
read(4, "", 65531) = 0
_llseek(3, 65, [65], SEEK_SET) = 0
_llseek(3, 66, [66], SEEK_SET) = 0
close(4) = 0
write(3, "ciao\n", 5) = 5
_llseek(3, 0, [0], SEEK_SET) = 0
write(3, "PK\3\4\n\0\0\0\0\0\321r1?h};\25\5\0\0\0\5\0\0\0\10\0\34\0ci"..., 66) = 66
_llseek(3, 71, [71], SEEK_SET) = 0
write(1, " (stored 0%)\n", 13 (stored 0%)
) = 13
write(3, "PK\1\2\36\3\n\0\0\0\0\0\321r1?h};\25\5\0\0\0\5\0\0\0\10\0\30\0"..., 100) = 100
close(3) = 0
lstat64("ciao.zip", 0xbf961600) = -1 ENOENT (No such file or directory)
rename("zijnRHbC", "ciao.zip") = 0
chmod("ciao.zip", 0100644) = 0
exit_group(0) = ?

If you want to know all the "open" commands, the do

strace -e open youcommand