mgrigorov in 🌐 euler-arm-22 in /tmp/variantbam/hh via 🅒 test123 took 10m40s
❯ file bin/* (test123)
bin/variant: ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
mgrigorov in 🌐 euler-arm-22 in /tmp/variantbam/hh via 🅒 test123
❯ ./bin/variant (test123)
Usage: variant <input.bam> [OPTIONS]
Description: Filter a BAM/SAM/CRAM/STDIN according to hierarchical rules
General options
-h, --help Display this help and exit
-v, --verbose Verbose output
-x, --no-output Don't output reads (used for profiling with -q)
-r, --rules JSON ecript for the rules.
-k, --proc-regions-file Samtools-style region string (e.g. 1:1,000-2,000) or BED/VCF of regions to process. -k UN iterates over unmapped-unmapped reads
-Q, --mark-as-qc-fail Flag reads that don't pass VariantBam with the failed QC flag, rather than deleting the read.
Output options
-o, --output Output file to write to (BAM/SAM/CRAM) file instead of stdout
-C, --cram Output file should be in CRAM format
-b, --bam Output should be in binary BAM format
-T, --reference Path to reference. Required for reading/writing CRAM
-s, --strip-tags Remove the specified tags, separated by commas. eg. -s RG,MD
-S, --strip-all-tags Remove all alignment tags
-Z, --write-trimmed Output the base-quality trimmed sequence rather than the original sequence. Also removes quality scores
Filtering options
-q, --qc-file Output a qc file that contains information about BAM
-m, --max-coverage Maximum coverage of output file. BAM must be sorted. Negative values enforce a minimum coverage
-p, --min-phred Set the minimum base quality score considered to be high-quality
Region specifiers
-g, --region Regions (e.g. myvcf.vcf or WG for whole genome) or newline seperated subsequence file.
-G, --exclude-region Same as -g, but for region where satisfying a rule EXCLUDES this read.
-l, --linked-region Same as -g, but turns on mate-linking
-L, --linked-exclude-region Same as -l, but for mate-linked region where satisfying this rule EXCLUDES this read.
-P, --region-pad Apply a padding to each region supplied with the region flags (specify after region flag)
Command line rules shortcuts (to be used without supplying a -r script)
--min-clip Minimum number of quality clipped bases
--max-nbases Maximum number of N bases
--min-mapq Minimum mapping quality
--min-del Minimum number of deleted bases
--min-ins Minimum number of inserted bases
--min-length Minimum read length (after base-quality trimming)
--motif Motif file
-R, --read-group Limit to just a single read group
-f, --include-aln-flag Flags to include (like samtools -f)
-F, --exclude-aln-flag Flags to exclude (like samtools -F)
But ./bin/variant --help (and any other attempt to pass an argument, e.g. -v or -b) hangs. strace produces:
mgrigorov in 🌐 euler-arm-22 in /tmp/variantbam/hh via 🅒 test123
❯ strace ./bin/variant -h (test123)
execve("./bin/variant", ["./bin/variant", "-h"], 0xffffd2535418 /* 40 vars */) = 0
brk(NULL) = 0xaaaafa07e000
readlinkat(AT_FDCWD, "/proc/self/exe", "/tmp/variantbam/hh/bin/variant", 4096) = 30
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xffff86e9f000
faccessat(AT_FDCWD, "/etc/ld.so.preload", R_OK) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/aarch64/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/aarch64/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/aarch64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/aarch64/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/tls/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/aarch64/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/aarch64/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/aarch64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/aarch64/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/tmp/variantbam/hh/bin/../lib/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/aarch64/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/aarch64/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/aarch64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/aarch64/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/tls/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/aarch64/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/aarch64/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/aarch64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/aarch64/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/", {st_mode=S_IFDIR|0755, st_size=4096, ...}, 0) = 0
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/aarch64/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/aarch64/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/aarch64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/aarch64/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/tls/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/aarch64/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/aarch64/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/aarch64/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/aarch64/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/atomics/libz.so.1", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
newfstatat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/atomics/", 0xfffff90b9cb0, 0) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/libz.so.1", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0\267\0\1\0\0\0\0\0\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=143448, ...}) = 0
mmap(NULL, 196624, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff86e35000
mprotect(0xffff86e50000, 81920, PROT_NONE) = 0
mmap(0xffff86e64000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1f000) = 0xffff86e64000
close(3) = 0
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/libbz2.so.1.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/libbz2.so.1.0", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0\267\0\1\0\0\0\0\0\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=281576, ...}) = 0
mmap(NULL, 199712, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff86e04000
mprotect(0xffff86e15000, 122880, PROT_NONE) = 0
mmap(0xffff86e33000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1f000) = 0xffff86e33000
close(3) = 0
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/liblzma.so.5", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/liblzma.so.5", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0\267\0\1\0\0\0\240;\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0775, st_size=197448, ...}) = 0
mmap(NULL, 237584, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff86dc9000
mprotect(0xffff86df2000, 65536, PROT_NONE) = 0
mmap(0xffff86e02000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x29000) = 0xffff86e02000
close(3) = 0
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/libstdc++.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0\267\0\1\0\0\0\20\335\t\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=2296824, ...}) = 0
mmap(NULL, 2373152, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff86b85000
mprotect(0xffff86d9d000, 110592, PROT_NONE) = 0
mmap(0xffff86db8000, 57344, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x223000) = 0xffff86db8000
mmap(0xffff86dc6000, 9760, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0xffff86dc6000
close(3) = 0
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/libm.so.6", O_RDONLY|O_CLOEXEC) = -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=46015, ...}) = 0
mmap(NULL, 46015, PROT_READ, MAP_PRIVATE, 3, 0) = 0xffff86e93000
close(3) = 0
openat(AT_FDCWD, "/usr/lib64/libm.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0\267\0\1\0\0\0p\333\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=591984, ...}) = 0
mmap(NULL, 655384, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff86ae4000
mprotect(0xffff86b67000, 114688, PROT_NONE) = 0
mmap(0xffff86b83000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x8f000) = 0xffff86b83000
close(3) = 0
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/libgcc_s.so.1", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\0\0\0\0\0\0\0\0\0\3\0\267\0\1\0\0\0\260+\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=133328, ...}) = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xffff86e91000
mmap(NULL, 197328, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff86ab3000
mprotect(0xffff86ac7000, 110592, PROT_NONE) = 0
mmap(0xffff86ae2000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x1f000) = 0xffff86ae2000
close(3) = 0
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib64/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\267\0\1\0\0\0\320\7\0\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=67632, ...}) = 0
mmap(NULL, 131088, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff86a92000
mprotect(0xffff86a93000, 122880, PROT_NONE) = 0
mmap(0xffff86ab1000, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0xf000) = 0xffff86ab1000
close(3) = 0
openat(AT_FDCWD, "/opt/openEuler/gcc-toolset-12/root/usr/lib64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/home/mgrigorov/miniconda3/envs/test123/lib/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
openat(AT_FDCWD, "/usr/lib64/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\267\0\1\0\0\0P\262\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_mode=S_IFREG|0755, st_size=1661256, ...}) = 0
mmap(NULL, 1764352, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0xffff868e3000
mprotect(0xffff86a67000, 102400, PROT_NONE) = 0
mmap(0xffff86a80000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x18d000) = 0xffff86a80000
mmap(0xffff86a86000, 48128, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0xffff86a86000
close(3) = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xffff86e8f000
set_tid_address(0xffff86e8f830) = 556779
set_robust_list(0xffff86e8f840, 24) = 0
mprotect(0xffff86a80000, 12288, PROT_READ) = 0
mprotect(0xffff86ab1000, 4096, PROT_READ) = 0
mprotect(0xffff86ae2000, 4096, PROT_READ) = 0
mprotect(0xffff86b83000, 4096, PROT_READ) = 0
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0xffff86e8d000
mprotect(0xffff86db8000, 53248, PROT_READ) = 0
mprotect(0xffff86e02000, 4096, PROT_READ) = 0
mprotect(0xffff86e33000, 4096, PROT_READ) = 0
mprotect(0xffff86e64000, 4096, PROT_READ) = 0
mprotect(0xaaaaba19c000, 16384, PROT_READ) = 0
mprotect(0xffff86ea4000, 8192, PROT_READ) = 0
prlimit64(0, RLIMIT_STACK, NULL, {rlim_cur=8192*1024, rlim_max=RLIM64_INFINITY}) = 0
munmap(0xffff86e93000, 46015) = 0
getrandom("\xb4\x09\x83\xe1\xc9\xdb\xbf\xf6", 8, GRND_NONBLOCK) = 8
brk(NULL) = 0xaaaafa07e000
brk(0xaaaafa09f000) = 0xaaaafa09f000
futex(0xffff86dc65a4, FUTEX_WAKE_PRIVATE, 2147483647) = 0
Hello,
I try to build a
linux-aarch64binary for Bioconda - https://github.com/bioconda/bioconda-recipes/pull/48763. I use https://github.com/DLTcollab/sse2neon/ to translate Intel SSE to ARM NEON.The build passes fine!
But
./bin/variant --help(and any other attempt to pass an argument, e.g.-vor-b) hangs.straceproduces:Any ideas what could be wrong ?