Assertion `compressBound(0xff00) < 0x10000' failed when using STAR 2.7.9a
RobAlbn opened this issue · comments
I am using STAR 2.7.9a. In the last two days, I am getting an error when running alignments with STAR (independently from the data and genome index I am using). What could be causing this error, which is reported in the next paragraph? Notably, STAR returns this error even when performing alignments that used to complete successfully in the past, before this issue started. Thank you very much for your attention and help on this!
INFO: localdir at /localscratch/8889241.roberto.albanese
INFO: your job will run on local system.
STAR: bgzf.c:158: bgzf_open: Assertion `compressBound(0xff00) < 0x10000' failed.
*** Aborted
Register dump:
RAX: 0000000000000000 RBX: 0000000000000006 RCX: 00007ffff684a37f
RDX: 0000000000000000 RSI: 00007ffffffdb580 RDI: 0000000000000002
RBP: 00007ffff699d5f8 R8 : 0000000000000000 R9 : 00007ffffffdb580
R10: 0000000000000008 R11: 0000000000000246 R12: 0000000000594eab
R13: 0000000000594f18 R14: 000000000000009e R15: 00007ffffffeb540
RSP: 00007ffffffdb580
RIP: 00007ffff684a37f EFLAGS: 00000246
CS: 0033 FS: 0000 GS: 0000
Trap: 00000000 Error: 00000000 OldMask: 00000000 CR2: 00000000
FPUCW: 0000037f FPUSW: 00000000 TAG: 00007fff
RIP: f76a5f3b RDP: 00000000
ST(0) 0000 0000000000000000 ST(1) 0000 0000000000000000
ST(2) 0000 0000000000000000 ST(3) 0000 0000000000000000
ST(4) 0000 0000000000000000 ST(5) 0000 0000000000000000
ST(6) ffff b000000000000000 ST(7) b000 b000000000000000
mxcsr: 1fa0
XMM0: 00000000000000000000000000000000 XMM1: 00000000000000000000000000000000
XMM2: 00000000000000000000000000000000 XMM3: 00000000000000000000000000000000
XMM4: 00000000000000000000000000000000 XMM5: 00000000000000000000000000000000
XMM6: 00000000000000000000000000000000 XMM7: 00000000000000000000000000000000
XMM8: 00000000000000000000000000000000 XMM9: 00000000000000000000000000000000
XMM10: 00000000000000000000000000000000 XMM11: 00000000000000000000000000000000
XMM12: 00000000000000000000000000000000 XMM13: 00000000000000000000000000000000
XMM14: 00000000000000000000000000000000 XMM15: 00000000000000000000000000000000
Backtrace:
/lib64/libc.so.6(gsignal+0x10f)[0x7ffff684a37f]
/lib64/libc.so.6(abort+0x127)[0x7ffff6834db5]
/lib64/libc.so.6(+0x21c89)[0x7ffff6834c89]
/lib64/libc.so.6(+0x2fa76)[0x7ffff6842a76]
/home/roberto.albanese/software/STAR-2.7.9a/bin/Linux_x86_64/STAR[0x53b3b0]
/home/roberto.albanese/software/STAR-2.7.9a/bin/Linux_x86_64/STAR[0x4af101]
/home/roberto.albanese/software/STAR-2.7.9a/bin/Linux_x86_64/STAR[0x40da52]
/lib64/libc.so.6(__libc_start_main+0xf3)[0x7ffff6836493]
/home/roberto.albanese/software/STAR-2.7.9a/bin/Linux_x86_64/STAR[0x419125]
Memory map:
00400000-005bc000 r-xp 00000000 00:48 4804921705 /home/roberto.albanese/software/STAR-2.7.9a/bin/Linux_x86_64/STAR
007bc000-007bd000 r--p 001bc000 00:48 4804921705 /home/roberto.albanese/software/STAR-2.7.9a/bin/Linux_x86_64/STAR
007bd000-007cb000 rw-p 001bd000 00:48 4804921705 /home/roberto.albanese/software/STAR-2.7.9a/bin/Linux_x86_64/STAR
007cb000-00832000 rw-p 00000000 00:00 0 [heap]
7ffff660f000-7ffff6612000 r-xp 00000000 08:02 36793927 /usr/lib64/libdl-2.28.so
7ffff6612000-7ffff6811000 ---p 00003000 08:02 36793927 /usr/lib64/libdl-2.28.so
7ffff6811000-7ffff6812000 r--p 00002000 08:02 36793927 /usr/lib64/libdl-2.28.so
7ffff6812000-7ffff6813000 rw-p 00003000 08:02 36793927 /usr/lib64/libdl-2.28.so
7ffff6813000-7ffff69cf000 r-xp 00000000 08:02 36776071 /usr/lib64/libc-2.28.so
7ffff69cf000-7ffff6bce000 ---p 001bc000 08:02 36776071 /usr/lib64/libc-2.28.so
7ffff6bce000-7ffff6bd2000 r--p 001bb000 08:02 36776071 /usr/lib64/libc-2.28.so
7ffff6bd2000-7ffff6bd4000 rw-p 001bf000 08:02 36776071 /usr/lib64/libc-2.28.so
7ffff6bd4000-7ffff6bd8000 rw-p 00000000 00:00 0
7ffff6bd8000-7ffff6bf3000 r-xp 00000000 08:02 37169965 /usr/lib64/libpthread-2.28.so
7ffff6bf3000-7ffff6df2000 ---p 0001b000 08:02 37169965 /usr/lib64/libpthread-2.28.so
7ffff6df2000-7ffff6df3000 r--p 0001a000 08:02 37169965 /usr/lib64/libpthread-2.28.so
7ffff6df3000-7ffff6df4000 rw-p 0001b000 08:02 37169965 /usr/lib64/libpthread-2.28.so
7ffff6df4000-7ffff6df8000 rw-p 00000000 00:00 0
7ffff6df8000-7ffff6e0f000 r-xp 00000000 08:02 100684981 /cm/local/apps/gcc/10.2.0/lib64/libgcc_s.so.1
7ffff6e0f000-7ffff700e000 ---p 00017000 08:02 100684981 /cm/local/apps/gcc/10.2.0/lib64/libgcc_s.so.1
7ffff700e000-7ffff700f000 r--p 00016000 08:02 100684981 /cm/local/apps/gcc/10.2.0/lib64/libgcc_s.so.1
7ffff700f000-7ffff7010000 rw-p 00017000 08:02 100684981 /cm/local/apps/gcc/10.2.0/lib64/libgcc_s.so.1
7ffff7010000-7ffff704e000 r-xp 00000000 08:02 100684988 /cm/local/apps/gcc/10.2.0/lib64/libgomp.so.1.0.0
7ffff704e000-7ffff724d000 ---p 0003e000 08:02 100684988 /cm/local/apps/gcc/10.2.0/lib64/libgomp.so.1.0.0
7ffff724d000-7ffff724e000 r--p 0003d000 08:02 100684988 /cm/local/apps/gcc/10.2.0/lib64/libgomp.so.1.0.0
7ffff724e000-7ffff724f000 rw-p 0003e000 08:02 100684988 /cm/local/apps/gcc/10.2.0/lib64/libgomp.so.1.0.0
7ffff724f000-7ffff73d0000 r-xp 00000000 08:02 36888910 /usr/lib64/libm-2.28.so
7ffff73d0000-7ffff75cf000 ---p 00181000 08:02 36888910 /usr/lib64/libm-2.28.so
7ffff75cf000-7ffff75d0000 r--p 00180000 08:02 36888910 /usr/lib64/libm-2.28.so
7ffff75d0000-7ffff75d1000 rw-p 00181000 08:02 36888910 /usr/lib64/libm-2.28.so
7ffff75d1000-7ffff7794000 r-xp 00000000 08:02 100685649 /cm/local/apps/gcc/10.2.0/lib64/libstdc++.so.6.0.28
7ffff7794000-7ffff7993000 ---p 001c3000 08:02 100685649 /cm/local/apps/gcc/10.2.0/lib64/libstdc++.so.6.0.28
7ffff7993000-7ffff799e000 r--p 001c2000 08:02 100685649 /cm/local/apps/gcc/10.2.0/lib64/libstdc++.so.6.0.28
7ffff799e000-7ffff79a1000 rw-p 001cd000 08:02 100685649 /cm/local/apps/gcc/10.2.0/lib64/libstdc++.so.6.0.28
7ffff79a1000-7ffff79a4000 rw-p 00000000 00:00 0
7ffff79a4000-7ffff79ca000 r-xp 00000000 00:89 7817491573 /share/sciswrepo/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/zlib-ng-2.0.0-qvhoazdgq5hmo6s32psbvmz75vofgtbt/lib/libz.so.1.2.11.zlib-ng
7ffff79ca000-7ffff7bc9000 ---p 00026000 00:89 7817491573 /share/sciswrepo/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/zlib-ng-2.0.0-qvhoazdgq5hmo6s32psbvmz75vofgtbt/lib/libz.so.1.2.11.zlib-ng
7ffff7bc9000-7ffff7bca000 r--p 00025000 00:89 7817491573 /share/sciswrepo/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/zlib-ng-2.0.0-qvhoazdgq5hmo6s32psbvmz75vofgtbt/lib/libz.so.1.2.11.zlib-ng
7ffff7bca000-7ffff7bcb000 rw-p 00026000 00:89 7817491573 /share/sciswrepo/spack/latest-2024-01-17/linux-centos8-skylake_avx512/gcc-8.4.1/zlib-ng-2.0.0-qvhoazdgq5hmo6s32psbvmz75vofgtbt/lib/libz.so.1.2.11.zlib-ng
7ffff7bcb000-7ffff7bcf000 r-xp 00000000 08:02 36760911 /usr/lib64/libSegFault.so
7ffff7bcf000-7ffff7dce000 ---p 00004000 08:02 36760911 /usr/lib64/libSegFault.so
7ffff7dce000-7ffff7dcf000 r--p 00003000 08:02 36760911 /usr/lib64/libSegFault.so
7ffff7dcf000-7ffff7dd0000 rw-p 00004000 08:02 36760911 /usr/lib64/libSegFault.so
7ffff7dd0000-7ffff7dfc000 r-xp 00000000 08:02 36760102 /usr/lib64/ld-2.28.so
7ffff7fd7000-7ffff7fdd000 rw-p 00000000 00:00 0
7ffff7fef000-7ffff7ff6000 rw-p 00000000 00:00 0
7ffff7ff6000-7ffff7ffa000 r--p 00000000 00:00 0 [vvar]
7ffff7ffa000-7ffff7ffc000 r-xp 00000000 00:00 0 [vdso]
7ffff7ffc000-7ffff7ffd000 r--p 0002c000 08:02 36760102 /usr/lib64/ld-2.28.so
7ffff7ffd000-7ffff7fff000 rw-p 0002d000 08:02 36760102 /usr/lib64/ld-2.28.so
7ffffffcd000-7ffffffff000 rw-p 00000000 00:00 0 [stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
/cm/local/apps/slurm/var/spool/job8889241/slurm_script: line 18: 3742255 Aborted (core dumped)
bgzf.c:158: bgzf_open: Assertion `compressBound(0xff00) < 0x10000' failed.
Upstream HTSlib users encountered this problem when HTSlib was used in conjunction with zlib-ng, which has slightly worse worst-case compression behaviour than the original zlib. See samtools/htslib#1257.
Whether @RobAlbn is also using zlib-ng or has managed to have a slightly too-big compressed block for some particular input data in some other way, the same zlib-ng-supporting fix will resolve the issue because it removed these assertions in favour of recovering when the HTSlib code actually encounters an oversized compressed block.
STAR bundles a pre-historic copy of HTSlib that predates this fix. So you would need update your copy at least to include the fix in samtools/htslib#1258 and/or ideally enable STAR to be built against an external unbundled HTSlib.
Thank you very much for your answer @jmarshall!
@RobAlbn: I also provided suggestions for workarounds in the meantime on your bioinf.SE posting.
Thank you for those suggestions too @jmarshall
@RobAlbn: STAR has not yet been updated, and @alexdobin has not yet weighed in on your bug report. I would recommend leaving this issue open so that this STAR problem can be tracked.