wrpearson/fasta36

*** stack smashing detected ***: terminated on the ENA PRO division

Opened this issue · 9 comments

olivierfriard commented

Dear Prof. Pearson,

I downloaded the PRO division from the ENA db (file STD_PRO_*.dat.gz in EMBL format) and gunziped them.
and wrote the STD_PRO.dtb file:
STD_PROD_1.dat 3
STD_PROD_2.dat 3
STD_PROD_3.dat 3

when I launch the following command on Ubuntu 20.04 32Gb RAM
fasta36 orf8.seq @STD_PRO.dtb > orf8_pro.fasta36

I obtained an error message this error message:
*** stack smashing detected ***: terminated
Aborted (core dumped)

The fasta version is 36.3.8h

Same error message for the HUM division, the VRL division is working.

Thank you for the support

Olivier Friard

wrpearson commented
olivierfriard commented

Hello,

I confirm that the issue is due to the EMBL format. If the EMBL db is converted in FASTA format the problem disappears.

I obtained from a colleague a more detailed error message:

AJ786203; Sulfolobus solfataricus small RNA ( 38) [r] 44 18.2 7.4e+07
AJ786177; Sulfolobus solfataricus non-codin ( 17) [r] 41 17.4 1.3e+08
More scores? [0]
Display alignments also? (y/n) [n] y
number of alignments [45791]?
*** ERROR [compacc2e.c:1015] - cannot allocate space[-883441658] for sequence encoding

Here some info about my system:

uname -a

Linux opti-9010 5.4.0-77-generic #86-Ubuntu SMP Thu Jun 17 02:35:03 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

cat /proc/cpuinfo

processor	: 0
vendor_id	: GenuineIntel
cpu family	: 6
model		: 58
model name	: Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz
stepping	: 9
microcode	: 0x21
cpu MHz		: 1995.064
cache size	: 8192 KB
physical id	: 0
siblings	: 8
core id		: 0
cpu cores	: 4
apicid		: 0
initial apicid	: 0
fpu		: yes
fpu_exception	: yes
cpuid level	: 13
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm cpuid_fault epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts md_clear flush_l1d
bugs		: cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass l1tf mds swapgs itlb_multihit srbds
bogomips	: 6784.51
clflush size	: 64
cache_alignment	: 64
address sizes	: 36 bits physical, 48 bits virtual
power management:

gcc -v

Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper
OFFLOAD_TARGET_NAMES=nvptx-none:hsa
OFFLOAD_TARGET_DEFAULT=1
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.3.0-17ubuntu1~20.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04)

Thank you for your support

Olivier Friard

wrpearson commented
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wrpearson commented
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wrpearson commented
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