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Save alperyilmaz/f0b13d32609f3fe4bac484c283b0b38e to your computer and use it in GitHub Desktop.
$ docker run --rm -v $(pwd)/data2:/data comics/bowtie2 wgsim -e 0 -N 10000 -1 300 -2 300 -r 0 -R 0 /data/s_cerevisiae.fa /data/sample_seq_1.fastq /data/sample_seq_2.fastq | |
[wgsim] seed = 1524818001 | |
[wgsim_core] calculating the total length of the reference sequence... | |
[wgsim_core] 18 sequences, total length: 12162995 | |
$ ls -alh data2 | |
total 25M | |
drwxr-xr-x 2 alper alper 4.0K Apr 27 11:32 . | |
drwxr-xr-x 4 alper alper 4.0K Apr 27 11:31 .. | |
-rw-r--r-- 1 root root 6.2M Apr 27 11:33 sample_seq_1.fastq | |
-rw-r--r-- 1 root root 6.2M Apr 27 11:33 sample_seq_2.fastq | |
-rw-r--r-- 1 alper alper 12M Apr 27 11:31 s_cerevisiae.fa | |
$ head GCF_000001405.38_GRCh38.p12_genomic.fna | |
>NC_000001.11 Homo sapiens chromosome 1, GRCh38.p12 Primary Assembly | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN | |
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN |
stat("/etc/perl/File/Spec/Unix.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/File/Spec/Unix.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/File/Spec/Unix.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/File/Spec/Unix.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/File/Spec/Unix.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/File/Spec/Unix.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/File/Spec/Unix.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/File/Spec/Unix.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/File/Spec/Unix.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/File/Spec/Unix.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/File/Spec/Unix.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/File/Spec/Unix.pm", {st_mode=S_IFREG|0644, st_size=10011, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/File/Spec/Unix.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package File::Spec::Unix;\n\nuse s"..., 8192) = 8192
brk(0x557bfcebf000) = 0x557bfcebf000
brk(0x557bfcee1000) = 0x557bfcee1000
read(4, "h\n if ( ! $self->file_name_is"..., 8192) = 1819
read(4, "", 8192) = 0
close(4) = 0
stat("/etc/perl/XSLoader.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/XSLoader.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/XSLoader.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/XSLoader.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/XSLoader.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/XSLoader.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/XSLoader.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/XSLoader.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/XSLoader.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/XSLoader.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/XSLoader.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/XSLoader.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/XSLoader.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/XSLoader.pm", {st_mode=S_IFREG|0644, st_size=3919, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/XSLoader.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "# Generated from XSLoader_pm.PL "..., 8192) = 3919
lseek(4, 3918, SEEK_SET) = 3918
lseek(4, 0, SEEK_CUR) = 3918
close(4) = 0
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Cwd/Cwd.bs", 0x557bfccc14f0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Cwd/Cwd.so", {st_mode=S_IFREG|0644, st_size=14528, ...}) = 0
futex(0x7fe77dbf00c8, FUTEX_WAKE_PRIVATE, 2147483647) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Cwd/Cwd.so", O_RDONLY|O_CLOEXEC) = 4
read(4, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\340\20\0\0\0\0\0\0"..., 832) = 832
fstat(4, {st_mode=S_IFREG|0644, st_size=14528, ...}) = 0
mmap(NULL, 2109776, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 4, 0) = 0x7fe77cc03000
mprotect(0x7fe77cc06000, 2093056, PROT_NONE) = 0
mmap(0x7fe77ce05000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 4, 0x2000) = 0x7fe77ce05000
close(4) = 0
mprotect(0x7fe77ce05000, 4096, PROT_READ) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
stat("/etc/perl/POSIX.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/POSIX.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/POSIX.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/POSIX.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/POSIX.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/POSIX.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/POSIX.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/POSIX.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/POSIX.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/POSIX.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/POSIX.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/POSIX.pm", {st_mode=S_IFREG|0644, st_size=20198, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/POSIX.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package POSIX;\nuse strict;\nuse w"..., 8192) = 8192
stat("/etc/perl/Fcntl.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Fcntl.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Fcntl.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Fcntl.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Fcntl.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Fcntl.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Fcntl.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Fcntl.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Fcntl.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Fcntl.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Fcntl.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Fcntl.pm", {st_mode=S_IFREG|0644, st_size=2156, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/Fcntl.pm", O_RDONLY) = 5
ioctl(5, TCGETS, 0x7ffe63a05120) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(5, 0, SEEK_CUR) = 0
brk(0x557bfcf02000) = 0x557bfcf02000
read(5, "package Fcntl;\n\nuse strict;\nour("..., 8192) = 2156
read(5, "", 8192) = 0
close(5) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Fcntl/Fcntl.bs", 0x557bfccc14f0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Fcntl/Fcntl.so", {st_mode=S_IFREG|0644, st_size=18456, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Fcntl/Fcntl.so", O_RDONLY|O_CLOEXEC) = 5
read(5, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\200\32\0\0\0\0\0\0"..., 832) = 832
fstat(5, {st_mode=S_IFREG|0644, st_size=18456, ...}) = 0
mmap(NULL, 2113784, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 5, 0) = 0x7fe77c9fe000
mprotect(0x7fe77ca01000, 2097152, PROT_NONE) = 0
mmap(0x7fe77cc01000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 5, 0x3000) = 0x7fe77cc01000
close(5) = 0
mprotect(0x7fe77cc01000, 4096, PROT_READ) = 0
brk(0x557bfcf23000) = 0x557bfcf23000
read(4, " {\n usage "printf(pattern, ar"..., 8192) = 8192
brk(0x557bfcf45000) = 0x557bfcf45000
read(4, "payloadsig issignaling) ],\n\n "..., 8192) = 3814
brk(0x557bfcf66000) = 0x557bfcf66000
read(4, "", 8192) = 0
close(4) = 0
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/POSIX/POSIX.bs", 0x557bfccc14f0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/POSIX/POSIX.so", {st_mode=S_IFREG|0644, st_size=105992, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/auto/POSIX/POSIX.so", O_RDONLY|O_CLOEXEC) = 4
read(4, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\320i\0\0\0\0\0\0"..., 832) = 832
fstat(4, {st_mode=S_IFREG|0644, st_size=105992, ...}) = 0
mmap(NULL, 2201160, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 4, 0) = 0x7fe77c7e4000
mprotect(0x7fe77c7fa000, 2097152, PROT_NONE) = 0
mmap(0x7fe77c9fa000, 16384, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 4, 0x16000) = 0x7fe77c9fa000
close(4) = 0
mprotect(0x7fe77c9fa000, 12288, PROT_READ) = 0
brk(0x557bfcf87000) = 0x557bfcf87000
stat("/etc/perl/Tie/Hash.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Tie/Hash.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Tie/Hash.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Tie/Hash.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Tie/Hash.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Tie/Hash.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Tie/Hash.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Tie/Hash.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Tie/Hash.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Tie/Hash.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Tie/Hash.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Tie/Hash.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Tie/Hash.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Tie/Hash.pm", {st_mode=S_IFREG|0644, st_size=2037, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/Tie/Hash.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package Tie::Hash;\n\nour $VERSION"..., 8192) = 2037
stat("/etc/perl/Carp.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Carp.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Carp.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Carp.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Carp.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Carp.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Carp.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Carp.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Carp.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Carp.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Carp.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Carp.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Carp.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Carp.pm", {st_mode=S_IFREG|0644, st_size=20148, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/Carp.pm", O_RDONLY) = 5
ioctl(5, TCGETS, 0x7ffe63a05120) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(5, 0, SEEK_CUR) = 0
read(5, "package Carp;\n\n{ use 5.006; }\nus"..., 8192) = 8192
brk(0x557bfcfa8000) = 0x557bfcfa8000
brk(0x557bfcfa7000) = 0x557bfcfa7000
read(5, "} @Args;\n\n if ($overf"..., 8192) = 8192
brk(0x557bfcfca000) = 0x557bfcfca000
read(5, "d_msg = " thread $tid" if $tid;\n"..., 8192) = 3764
brk(0x557bfcfeb000) = 0x557bfcfeb000
lseek(5, 20147, SEEK_SET) = 20147
lseek(5, 0, SEEK_CUR) = 20147
close(5) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
read(4, "", 8192) = 0
close(4) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
brk(0x557bfd00c000) = 0x557bfd00c000
brk(0x557bfd02d000) = 0x557bfd02d000
stat("/etc/perl/Sys/Hostname.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Sys/Hostname.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Sys/Hostname.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Sys/Hostname.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Sys/Hostname.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Sys/Hostname.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Sys/Hostname.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Sys/Hostname.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Sys/Hostname.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Sys/Hostname.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Sys/Hostname.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Sys/Hostname.pm", {st_mode=S_IFREG|0644, st_size=3571, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/Sys/Hostname.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package Sys::Hostname;\n\nuse stri"..., 8192) = 3571
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Sys/Hostname/Hostname.bs", 0x557bfccc14f0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Sys/Hostname/Hostname.so", {st_mode=S_IFREG|0644, st_size=6112, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/auto/Sys/Hostname/Hostname.so", O_RDONLY|O_CLOEXEC) = 5
read(5, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\0\10\0\0\0\0\0\0"..., 832) = 832
fstat(5, {st_mode=S_IFREG|0644, st_size=6112, ...}) = 0
mmap(NULL, 2101360, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 5, 0) = 0x7fe77c5e2000
mprotect(0x7fe77c5e3000, 2093056, PROT_NONE) = 0
mmap(0x7fe77c7e2000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 5, 0) = 0x7fe77c7e2000
close(5) = 0
mprotect(0x7fe77c7e2000, 4096, PROT_READ) = 0
lseek(4, 2894, SEEK_SET) = 2894
lseek(4, 0, SEEK_CUR) = 2894
close(4) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
stat("/etc/perl/Config.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Config.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Config.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Config.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Config.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Config.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Config.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Config.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Config.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Config.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Config.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Config.pm", {st_mode=S_IFREG|0644, st_size=3372, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/Config.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "# This file was created by confi"..., 8192) = 3372
brk(0x557bfd04e000) = 0x557bfd04e000
read(4, "", 8192) = 0
close(4) = 0
read(3, "\n\t"log-file=s" "..., 8192) = 8192
brk(0x557bfd06f000) = 0x557bfd06f000
stat("/etc/perl/File/Glob.pmc", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/etc/perl/File/Glob.pm", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/File/Glob.pmc", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/File/Glob.pm", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/File/Glob.pmc", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/File/Glob.pm", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/File/Glob.pmc", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/File/Glob.pm", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/File/Glob.pmc", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/File/Glob.pm", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/File/Glob.pmc", 0x7ffe63a058e0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/File/Glob.pm", {st_mode=S_IFREG|0644, st_size=2045, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/File/Glob.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05690) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package File::Glob;\n\nuse strict;"..., 8192) = 2045
lseek(4, 2044, SEEK_SET) = 2044
lseek(4, 0, SEEK_CUR) = 2044
close(4) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/File/Glob/Glob.bs", 0x557bfccc14f0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/auto/File/Glob/Glob.so", {st_mode=S_IFREG|0644, st_size=27088, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/auto/File/Glob/Glob.so", O_RDONLY|O_CLOEXEC) = 4
read(4, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\0\33\0\0\0\0\0\0"..., 832) = 832
fstat(4, {st_mode=S_IFREG|0644, st_size=27088, ...}) = 0
mmap(NULL, 2122256, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 4, 0) = 0x7fe77c3db000
mprotect(0x7fe77c3e1000, 2093056, PROT_NONE) = 0
mmap(0x7fe77c5e0000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 4, 0x5000) = 0x7fe77c5e0000
close(4) = 0
mprotect(0x7fe77c5e0000, 4096, PROT_READ) = 0
brk(0x557bfd092000) = 0x557bfd092000
read(3, "ot open --$i mate-1 output file "..., 8192) = 2987
read(3, "", 8192) = 0
close(3) = 0
brk(0x557bfd0b4000) = 0x557bfd0b4000
uname({sysname="Linux", nodename="ccd992e92b22", ...}) = 0
stat("/usr/bin/bowtie2", {st_mode=S_IFREG|0755, st_size=19371, ...}) = 0
lstat("/usr/bin/bowtie2", {st_mode=S_IFREG|0755, st_size=19371, ...}) = 0
stat("/etc/perl/Config_heavy.pl", 0x7ffe63a05c20) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Config_heavy.pl", 0x7ffe63a05c20) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Config_heavy.pl", 0x7ffe63a05c20) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Config_heavy.pl", 0x7ffe63a05c20) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Config_heavy.pl", 0x7ffe63a05c20) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Config_heavy.pl", {st_mode=S_IFREG|0644, st_size=54402, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/Config_heavy.pl", O_RDONLY) = 3
ioctl(3, TCGETS, 0x7ffe63a059d0) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(3, 0, SEEK_CUR) = 0
read(3, "# This file was created by confi"..., 8192) = 8192
read(3, "chlib=/usr/lib/x86_64-linux-gnu/"..., 8192) = 8192
read(3, " LONG_MAX=0x7fffffffffffffff"..., 8192) = 8192
read(3, "own='define'\nd_ldbl_dig='define'"..., 8192) = 8192
read(3, "/Perl/V Devel/SelfStubber Digest"..., 8192) = 8192
brk(0x557bfd0dd000) = 0x557bfd0dd000
brk(0x557bfd0d6000) = 0x557bfd0d6000
read(3, "-gnu /usr/lib/../lib /lib'\nlibs="..., 8192) = 8192
read(3, "ENTRANT_PROTO_B_IBW'\nstrings='/u"..., 8192) = 5250
read(3, "", 8192) = 0
close(3) = 0
brk(0x557bfd0fb000) = 0x557bfd0fb000
stat("/etc/perl/Config_git.pl", 0x7ffe63a05c10) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Config_git.pl", 0x7ffe63a05c10) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Config_git.pl", 0x7ffe63a05c10) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Config_git.pl", 0x7ffe63a05c10) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Config_git.pl", 0x7ffe63a05c10) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Config_git.pl", {st_mode=S_IFREG|0644, st_size=409, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/Config_git.pl", O_RDONLY) = 3
ioctl(3, TCGETS, 0x7ffe63a059c0) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(3, 0, SEEK_CUR) = 0
read(3, "################################"..., 8192) = 409
read(3, "", 8192) = 0
close(3) = 0
stat("/usr/bin/bowtie2-align-s", {st_mode=S_IFREG|0755, st_size=1616008, ...}) = 0
geteuid() = 0
pipe([3, 4]) = 0
pipe([5, 6]) = 0
clone(child_stack=NULL, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x7fe77de12290) = 7
close(6) = 0
close(4) = 0
read(5, "", 4) = 0
close(5) = 0
ioctl(3, TCGETS, 0x7ffe63a06130) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(3, 0, SEEK_CUR) = -1 ESPIPE (Illegal seek)
fcntl(3, F_SETFD, FD_CLOEXEC) = 0
read(3, "verbose\t0\nstartverbose\t0\nquiet\t0"..., 8192) = 325
read(3, "maxins\t1\nquals\t1\nQ1\t1\nQ2\t1\nrefid"..., 8192) = 1891
read(3, "", 8192) = 0
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=7, si_uid=0, si_status=0, si_utime=0, si_stime=1} ---
close(3) = 0
wait4(7, [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 7
openat(AT_FDCWD, ".", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
fstat(3, {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
getdents(3, /* 26 entries /, 32768) = 1040
lstat("hg18.1.bt2", {st_mode=S_IFREG|0755, st_size=961172069, ...}) = 0
lstat("hg18.2.bt2", {st_mode=S_IFREG|0755, st_size=717656024, ...}) = 0
lstat("hg18.3.bt2", {st_mode=S_IFREG|0755, st_size=76850, ...}) = 0
lstat("hg18.4.bt2", {st_mode=S_IFREG|0755, st_size=717656019, ...}) = 0
lstat("hg18.rev.1.bt2", {st_mode=S_IFREG|0755, st_size=961172069, ...}) = 0
lstat("hg18.rev.2.bt2", {st_mode=S_IFREG|0755, st_size=717656024, ...}) = 0
getdents(3, / 0 entries /, 32768) = 0
close(3) = 0
openat(AT_FDCWD, ".", O_RDONLY|O_NONBLOCK|O_CLOEXEC|O_DIRECTORY) = 3
fstat(3, {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
getdents(3, / 26 entries /, 32768) = 1040
getdents(3, / 0 entries */, 32768) = 0
close(3) = 0
stat("hg18.1.bt2l", 0x557bfccc14f0) = -1 ENOENT (No such file or directory)
pipe([3, 4]) = 0
rt_sigprocmask(SIG_BLOCK, [CHLD], [], 8) = 0
clone(child_stack=NULL, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x7fe77de12290) = 9
close(4) = 0
rt_sigaction(SIGINT, {sa_handler=SIG_IGN, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fe77d442890}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGQUIT, {sa_handler=SIG_IGN, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fe77d442890}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
wait4(9, Killed
[{WIFEXITED(s) && WEXITSTATUS(s) == 137}], 0, NULL) = 9
rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=9, si_uid=0, si_status=137, si_utime=0, si_stime=0} ---
rt_sigaction(SIGINT, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fe77d442890}, NULL, 8) = 0
rt_sigaction(SIGQUIT, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fe77d442890}, NULL, 8) = 0
read(3, "", 4) = 0
close(3) = 0
write(2, "(ERR): bowtie2-align exited with"..., 43(ERR): bowtie2-align exited with value 137
) = 43
rt_sigaction(SIGHUP, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGINT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fe77d442890}, 8) = 0
rt_sigaction(SIGQUIT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=SA_RESTORER, sa_restorer=0x7fe77d442890}, 8) = 0
rt_sigaction(SIGILL, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGTRAP, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGABRT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGBUS, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGFPE, NULL, {sa_handler=SIG_IGN, sa_mask=[FPE], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fe77d07df20}, 8) = 0
rt_sigaction(SIGKILL, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGUSR1, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGSEGV, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGUSR2, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGPIPE, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGALRM, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGTERM, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGSTKFLT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGCHLD, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGCONT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGSTOP, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGTSTP, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGTTIN, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGTTOU, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGURG, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGXCPU, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGXFSZ, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGVTALRM, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGPROF, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGWINCH, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGIO, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGPWR, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGSYS, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_2, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_3, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_4, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_5, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_6, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_7, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_8, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_9, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_10, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_11, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_12, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_13, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_14, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_15, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_16, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_17, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_18, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_19, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_20, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_21, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_22, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_23, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_24, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_25, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_26, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_27, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_28, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_29, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_30, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_31, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGRT_32, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGABRT, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGCHLD, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGIO, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
rt_sigaction(SIGSYS, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
exit_group(137) = ?
+++ exited with 137 +++
Satırların birinde hg18.1.bt2l
dosyası için sorgu yapıyor, ama bulamıyor. Bunun için mi öldürülüyor yoksa başka bir sorun mu var, tam kesin değil. .bt2l
sorunu için önerilen çözüm bowtie2'nin eski sürümlerini (< v2.2.8) kullanmak.
Ama ben hala memory sorunundan şüpheleniyorum, Docker for Windows Hyper-V üzerinden çalıştığı için RAM'ın hepsini kullandırtmıyor diye belirten forum yazıları var.
İlk önce memory meselesini deneyelim: Docker'a 5gb memory kullanmasını söyleyelim
docker run --memory 5g --rm -v A:\Homosapiens:/data alperyilmaz/bowtie2-samtools bowtie2 -x hg18 -1 h.sapiens_seq_1.fastq -2 h.sapiens_seq_2.fastq -S output1.sam
docker run --memory 5g --rm -v A:\Homosapiens:/data alperyilmaz/bowtie2-samtools bowtie2 -
x hg18 -1 h.sapiens_seq_1.fastq -2 h.sapiens_seq_2.fastq -S output1.sam
Killed
(ERR): bowtie2-align exited with value 137
docker run --security-opt seccomp:unconfined --rm -v A:\Homosapiens:/data alperyilmaz/bowt
ie2-samtools strace bowtie2 -x hg18 -1 h.sapiens_seq_1.fastq -2 h.sapiens_seq_2.fastq -S output1.sam
execve("/usr/bin/bowtie2", ["bowtie2", "-x", "hg18", "-1", "h.sapiens_seq_1.fastq", "-2", "h.sapiens_seq_2.fastq", "-S", "output1.sam"], 0x7ffce0694450 /* 3 vars /) = 0
brk(NULL) = 0x55e68dd09000
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=10944, ...}) = 0
mmap(NULL, 10944, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f867a475000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\260\34\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=2030544, ...}) = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f867a473000
mmap(NULL, 4131552, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f8679e60000
mprotect(0x7f867a047000, 2097152, PROT_NONE) = 0
mmap(0x7f867a247000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1e7000) = 0x7f867a247000
mmap(0x7f867a24d000, 15072, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f867a24d000
close(3) = 0
arch_prctl(ARCH_SET_FS, 0x7f867a474540) = 0
mprotect(0x7f867a247000, 16384, PROT_READ) = 0
mprotect(0x55e68c996000, 4096, PROT_READ) = 0
mprotect(0x7f867a478000, 4096, PROT_READ) = 0
munmap(0x7f867a475000, 10944) = 0
brk(NULL) = 0x55e68dd09000
brk(0x55e68dd2a000) = 0x55e68dd2a000
execve("/usr/local/sbin/perl", ["perl", "/usr/bin/bowtie2", "-x", "hg18", "-1", "h.sapiens_seq_1.fastq", "-2", "h.sapiens_seq_2.fastq", "-S", "output1.sam"], 0x7fff3e277b98 / 3 vars /) = -1 ENOENT (No such file or directory)
execve("/usr/local/bin/perl", ["perl", "/usr/bin/bowtie2", "-x", "hg18", "-1", "h.sapiens_seq_1.fastq", "-2", "h.sapiens_seq_2.fastq", "-S", "output1.sam"], 0x7fff3e277b98 / 3 vars /) = -1 ENOENT (No such file or directory)
execve("/usr/sbin/perl", ["perl", "/usr/bin/bowtie2", "-x", "hg18", "-1", "h.sapiens_seq_1.fastq", "-2", "h.sapiens_seq_2.fastq", "-S", "output1.sam"], 0x7fff3e277b98 / 3 vars /) = -1 ENOENT (No such file or directory)
execve("/usr/bin/perl", ["perl", "/usr/bin/bowtie2", "-x", "hg18", "-1", "h.sapiens_seq_1.fastq", "-2", "h.sapiens_seq_2.fastq", "-S", "output1.sam"], 0x7fff3e277b98 / 3 vars /) = 0
brk(NULL) = 0x557bfccc1000
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
access("/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=10944, ...}) = 0
mmap(NULL, 10944, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7fe77de15000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libdl.so.2", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0P\16\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0644, st_size=14560, ...}) = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fe77de13000
mmap(NULL, 2109712, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7fe77d9ed000
mprotect(0x7fe77d9f0000, 2093056, PROT_NONE) = 0
mmap(0x7fe77dbef000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x2000) = 0x7fe77dbef000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libm.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\200\272\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0644, st_size=1700792, ...}) = 0
mmap(NULL, 3789144, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7fe77d64f000
mprotect(0x7fe77d7ec000, 2093056, PROT_NONE) = 0
mmap(0x7fe77d9eb000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x19c000) = 0x7fe77d9eb000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libpthread.so.0", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0000b\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=144976, ...}) = 0
mmap(NULL, 2221184, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7fe77d430000
mprotect(0x7fe77d44a000, 2093056, PROT_NONE) = 0
mmap(0x7fe77d649000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x19000) = 0x7fe77d649000
mmap(0x7fe77d64b000, 13440, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7fe77d64b000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\260\34\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=2030544, ...}) = 0
mmap(NULL, 4131552, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7fe77d03f000
mprotect(0x7fe77d226000, 2097152, PROT_NONE) = 0
mmap(0x7fe77d426000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1e7000) = 0x7fe77d426000
mmap(0x7fe77d42c000, 15072, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7fe77d42c000
close(3) = 0
access("/etc/ld.so.nohwcap", F_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/lib/x86_64-linux-gnu/libcrypt.so.1", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0P\r\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0644, st_size=39208, ...}) = 0
mmap(NULL, 2322976, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7fe77ce07000
mprotect(0x7fe77ce10000, 2093056, PROT_NONE) = 0
mmap(0x7fe77d00f000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x8000) = 0x7fe77d00f000
mmap(0x7fe77d011000, 184864, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7fe77d011000
close(3) = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fe77de11000
arch_prctl(ARCH_SET_FS, 0x7fe77de11fc0) = 0
mprotect(0x7fe77d426000, 16384, PROT_READ) = 0
mprotect(0x7fe77d00f000, 4096, PROT_READ) = 0
mprotect(0x7fe77d649000, 4096, PROT_READ) = 0
mprotect(0x7fe77d9eb000, 4096, PROT_READ) = 0
mprotect(0x7fe77dbef000, 4096, PROT_READ) = 0
mprotect(0x557bfafb9000, 24576, PROT_READ) = 0
mprotect(0x7fe77de18000, 4096, PROT_READ) = 0
munmap(0x7fe77de15000, 10944) = 0
set_tid_address(0x7fe77de12290) = 6
set_robust_list(0x7fe77de122a0, 24) = 0
rt_sigaction(SIGRTMIN, {sa_handler=0x7fe77d435cb0, sa_mask=[], sa_flags=SA_RESTORER|SA_SIGINFO, sa_restorer=0x7fe77d442890}, NULL, 8) = 0
rt_sigaction(SIGRT_1, {sa_handler=0x7fe77d435d50, sa_mask=[], sa_flags=SA_RESTORER|SA_RESTART|SA_SIGINFO, sa_restorer=0x7fe77d442890}, NULL, 8) = 0
rt_sigprocmask(SIG_UNBLOCK, [RTMIN RT_1], NULL, 8) = 0
prlimit64(0, RLIMIT_STACK, NULL, {rlim_cur=81921024, rlim_max=RLIM64_INFINITY}) = 0
rt_sigaction(SIGFPE, {sa_handler=SIG_IGN, sa_mask=[FPE], sa_flags=SA_RESTORER|SA_RESTART, sa_restorer=0x7fe77d07df20}, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
brk(NULL) = 0x557bfccc1000
brk(0x557bfcce2000) = 0x557bfcce2000
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
openat(AT_FDCWD, "/dev/urandom", O_RDONLY) = 3
read(3, "\347\250G\375", 4) = 4
close(3) = 0
readlink("/proc/self/exe", "/usr/bin/perl", 4095) = 13
stat("/usr/lib/x86_64-linux-gnu/perl-base/5.26.1/x86_64-linux-gnu-thread-multi", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl-base/5.26.1", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/site_perl/5.26.1/x86_64-linux-gnu-thread-multi", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/site_perl/5.26.1", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/site_perl/x86_64-linux-gnu-thread-multi", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.0", 0x7ffe63a062f0) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.0", 0x7ffe63a062f0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl-base/5.26.0", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl-base/5.26.0/x86_64-linux-gnu-thread-multi", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl-base/x86_64-linux-gnu-thread-multi", 0x7ffe63a060c0) = -1 ENOENT (No such file or directory)
ioctl(0, TCGETS, 0x7ffe63a05ea0) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(0, 0, SEEK_CUR) = -1 ESPIPE (Illegal seek)
ioctl(1, TCGETS, 0x7ffe63a05ea0) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(1, 0, SEEK_CUR) = -1 ESPIPE (Illegal seek)
ioctl(2, TCGETS, 0x7ffe63a05eb0) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(2, 0, SEEK_CUR) = -1 ESPIPE (Illegal seek)
openat(AT_FDCWD, "/usr/bin/bowtie2", O_RDONLY) = 3
ioctl(3, TCGETS, 0x7ffe63a05fb0) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(3, 0, SEEK_CUR) = 0
fcntl(3, F_SETFD, FD_CLOEXEC) = 0
fstat(3, {st_mode=S_IFREG|0755, st_size=19371, ...}) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
rt_sigaction(SIGCHLD, NULL, {sa_handler=SIG_DFL, sa_mask=[], sa_flags=0}, 8) = 0
brk(0x557bfcd03000) = 0x557bfcd03000
read(3, "#!/usr/bin/env perl\n\n#\n# Copyrig"..., 8192) = 8192
stat("/etc/perl/strict.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/strict.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/strict.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/strict.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/strict.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/strict.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/strict.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/strict.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/strict.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/strict.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/strict.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/strict.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/strict.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/strict.pm", {st_mode=S_IFREG|0644, st_size=1606, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/strict.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package strict;\n\n$strict::VERSIO"..., 8192) = 1606
lseek(4, 1605, SEEK_SET) = 1605
lseek(4, 0, SEEK_CUR) = 1605
close(4) = 0
stat("/etc/perl/warnings.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/warnings.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/warnings.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/warnings.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/warnings.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/warnings.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/warnings.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/warnings.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/warnings.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/warnings.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/warnings.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/warnings.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/warnings.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/warnings.pm", {st_mode=S_IFREG|0644, st_size=21950, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/warnings.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "# -- buffer-read-only: t --\n# "..., 8192) = 8192
brk(0x557bfcd24000) = 0x557bfcd24000
read(4, "# [38]\n 'severe'\t\t\t\t=> "\x00\"..., 8192) = 8192
read(4, "\x00\x00\x00\x00\x00\x00\x08\x00"..., 8192) = 5566
brk(0x557bfcd46000) = 0x557bfcd46000
lseek(4, 21870, SEEK_SET) = 21870
lseek(4, 0, SEEK_CUR) = 21870
close(4) = 0
stat("/etc/perl/Getopt/Long.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Getopt/Long.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Getopt/Long.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Getopt/Long.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Getopt/Long.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Getopt/Long.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Getopt/Long.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Getopt/Long.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Getopt/Long.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Getopt/Long.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Getopt/Long.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Getopt/Long.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Getopt/Long.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Getopt/Long.pm", {st_mode=S_IFREG|0644, st_size=43325, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/Getopt/Long.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "#! perl\n\n# Getopt::Long.pm -- Un"..., 8192) = 8192
stat("/etc/perl/vars.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/etc/perl/vars.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/vars.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/vars.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/vars.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/vars.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/vars.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/vars.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/vars.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/vars.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/vars.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/vars.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/vars.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/vars.pm", {st_mode=S_IFREG|0644, st_size=1149, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/vars.pm", O_RDONLY) = 5
ioctl(5, TCGETS, 0x7ffe63a05120) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(5, 0, SEEK_CUR) = 0
read(5, "package vars;\n\nuse 5.006;\n\nour $"..., 8192) = 1149
stat("/etc/perl/warnings/register.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/warnings/register.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/warnings/register.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/warnings/register.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/warnings/register.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/warnings/register.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/warnings/register.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/warnings/register.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/warnings/register.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/warnings/register.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/warnings/register.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/warnings/register.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/warnings/register.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/warnings/register.pm", {st_mode=S_IFREG|0644, st_size=488, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/warnings/register.pm", O_RDONLY) = 6
ioctl(6, TCGETS, 0x7ffe63a04a20) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(6, 0, SEEK_CUR) = 0
read(6, "package warnings::register;\n\nour"..., 8192) = 488
brk(0x557bfcd67000) = 0x557bfcd67000
lseek(6, 487, SEEK_SET) = 487
lseek(6, 0, SEEK_CUR) = 487
close(6) = 0
lseek(5, 1148, SEEK_SET) = 1148
lseek(5, 0, SEEK_CUR) = 1148
close(5) = 0
stat("/etc/perl/Exporter.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Exporter.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Exporter.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Exporter.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Exporter.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Exporter.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Exporter.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Exporter.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Exporter.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Exporter.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Exporter.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Exporter.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Exporter.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Exporter.pm", {st_mode=S_IFREG|0644, st_size=2367, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/Exporter.pm", O_RDONLY) = 5
ioctl(5, TCGETS, 0x7ffe63a05120) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(5, 0, SEEK_CUR) = 0
read(5, "package Exporter;\n\nrequire 5.006"..., 8192) = 2367
lseek(5, 2366, SEEK_SET) = 2366
lseek(5, 0, SEEK_CUR) = 2366
close(5) = 0
brk(0x557bfcd88000) = 0x557bfcd88000
stat("/etc/perl/constant.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/etc/perl/constant.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/constant.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/constant.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/constant.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/constant.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/constant.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/constant.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/constant.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/constant.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/constant.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/constant.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/constant.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/constant.pm", {st_mode=S_IFREG|0644, st_size=5737, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/constant.pm", O_RDONLY) = 5
ioctl(5, TCGETS, 0x7ffe63a05120) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(5, 0, SEEK_CUR) = 0
read(5, "package constant;\nuse 5.008;\nuse"..., 8192) = 5737
brk(0x557bfcdac000) = 0x557bfcdac000
lseek(5, 5736, SEEK_SET) = 5736
lseek(5, 0, SEEK_CUR) = 5736
close(5) = 0
read(4, "= 0;\n\tprint STDERR\n\t ("Getopt::"..., 8192) = 8192
brk(0x557bfcdd0000) = 0x557bfcdd0000
read(4, "}) eq 'ARRAY' ) {\n\t\t\tprint STDER"..., 8192) = 8192
brk(0x557bfcdf1000) = 0x557bfcdf1000
read(4, " foreach ( @NAMEs ) {\n\n\t$_ = "..., 8192) = 8192
brk(0x557bfce13000) = 0x557bfce13000
read(4, "sh back.\n\t unshift (@$argv, $"..., 8192) = 8192
brk(0x557bfce37000) = 0x557bfce37000
brk(0x557bfce5b000) = 0x557bfce5b000
read(4, ""NOEXIT" || $pa->{-exitval} < 2)"..., 8192) = 2365
stat("/etc/perl/overload.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/etc/perl/overload.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/overload.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/overload.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/overload.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/overload.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/overload.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/overload.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/overload.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/overload.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/overload.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/overload.pm", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/overload.pmc", 0x7ffe63a05370) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/overload.pm", {st_mode=S_IFREG|0644, st_size=4441, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/overload.pm", O_RDONLY) = 5
ioctl(5, TCGETS, 0x7ffe63a05120) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(5, 0, SEEK_CUR) = 0
read(5, "package overload;\n\nour $VERSION "..., 8192) = 4441
brk(0x557bfce7c000) = 0x557bfce7c000
stat("/etc/perl/overloading.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/overloading.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/overloading.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/overloading.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/overloading.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/overloading.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/overloading.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/overloading.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/overloading.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/overloading.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/overloading.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/overloading.pm", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/overloading.pmc", 0x7ffe63a04c70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/overloading.pm", {st_mode=S_IFREG|0644, st_size=964, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/overloading.pm", O_RDONLY) = 6
ioctl(6, TCGETS, 0x7ffe63a04a20) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(6, 0, SEEK_CUR) = 0
read(6, "package overloading;\nuse warning"..., 8192) = 964
lseek(6, 963, SEEK_SET) = 963
lseek(6, 0, SEEK_CUR) = 963
close(6) = 0
lseek(5, 4440, SEEK_SET) = 4440
lseek(5, 0, SEEK_CUR) = 4440
close(5) = 0
brk(0x557bfce9e000) = 0x557bfce9e000
read(4, "", 8192) = 0
close(4) = 0
getuid() = 0
geteuid() = 0
getgid() = 0
getegid() = 0
stat("/etc/perl/Exporter/Heavy.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/Exporter/Heavy.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Exporter/Heavy.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/Exporter/Heavy.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Exporter/Heavy.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/Exporter/Heavy.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Exporter/Heavy.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/Exporter/Heavy.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Exporter/Heavy.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/Exporter/Heavy.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Exporter/Heavy.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/Exporter/Heavy.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Exporter/Heavy.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl/5.26/Exporter/Heavy.pm", {st_mode=S_IFREG|0644, st_size=6406, ...}) = 0
openat(AT_FDCWD, "/usr/share/perl/5.26/Exporter/Heavy.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package Exporter::Heavy;\n\nuse st"..., 8192) = 6406
read(4, "", 8192) = 0
close(4) = 0
stat("/etc/perl/File/Spec.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/etc/perl/File/Spec.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/File/Spec.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/lib/x86_64-linux-gnu/perl/5.26.1/File/Spec.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/File/Spec.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/local/share/perl/5.26.1/File/Spec.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/File/Spec.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl5/5.26/File/Spec.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/File/Spec.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/share/perl5/File/Spec.pm", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/File/Spec.pmc", 0x7ffe63a05a70) = -1 ENOENT (No such file or directory)
stat("/usr/lib/x86_64-linux-gnu/perl/5.26/File/Spec.pm", {st_mode=S_IFREG|0644, st_size=619, ...}) = 0
openat(AT_FDCWD, "/usr/lib/x86_64-linux-gnu/perl/5.26/File/Spec.pm", O_RDONLY) = 4
ioctl(4, TCGETS, 0x7ffe63a05820) = -1 ENOTTY (Inappropriate ioctl for device)
lseek(4, 0, SEEK_CUR) = 0
read(4, "package File::Spec;\n\nuse strict;"..., 8192) = 619
lseek(4, 618, SEEK_SET) = 618
lseek(4, 0, SEEK_CUR) = 618
close(4) = 0