bowtie test

comic-test

$ 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