Package: ncbi-blast+ Version: 2.8.1-1 Severity: important Dear Maintainer,
* What led up to the situation? Running commands like one of the following: blastn -query test.fasta -subject test.fasta makeblastdb -dbtype nucl -in test.fasta * What was the outcome of this action? A runtime trap with a message 'Instruction non permise' (sorry for the french message, got the same in a LANG=C env) Here are extracts from dmesg: [16975777.040241] traps: blastn[16028] trap invalid opcode ip:7f5c96a4598c sp:7ffece18a380 error:0 in libblast.so[7f5c96a04000+66000] [16976213.970602] traps: makeblastdb[17484] trap invalid opcode ip:7fca6c0bfb02 sp:7ffe3fae78a0 error:0 in libxutil.so[7fca6c08c000+83000] and here is the output got using gdb and ncbi-blast+-dbgsym: gdb --args blastn -query test.fasta -subject test.fasta GNU gdb (Debian 8.2.1-2+b3) 8.2.1 Copyright (C) 2018 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word"... Reading symbols from blastn...Reading symbols from /usr/lib/debug/.build-id/00/382f3290f9ed8c1cace9c6e03d714c031cbd3d.debug...done. done. (gdb) go Command requires an argument. (gdb) run Starting program: /usr/bin/blastn -query test.fasta -subject test.fasta [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". BLASTN 2.8.1+ Program received signal SIGILL, Illegal instruction. 0x00007ffff7afe98c in BLAST_ComputeLengthAdjustment (K=<optimized out>, logK=-0.77652878949899629, alpha_d_lambda=1.171875, beta=-2, query_length=query_length@entry=86, db_length=db_length@entry=86, db_num_seqs=db_num_seqs@entry=1, length_adjustment=length_adjustment@entry=0x7fffffffcf84) at ./c++/src/algo/blast/core/blast_stat.c:5093 5093 ./c++/src/algo/blast/core/blast_stat.c: No such file or directory. (gdb) The CPU info of the hardware used to run the commands is: # lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian Address sizes: 40 bits physical, 48 bits virtual CPU(s): 16 On-line CPU(s) list: 0-15 Thread(s) per core: 2 Core(s) per socket: 2 Socket(s): 4 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 15 Model: 6 Model name: Intel(R) Xeon(TM) CPU 3.40GHz Stepping: 8 CPU MHz: 3391.598 BogoMIPS: 6783.19 Virtualization: VT-x L1d cache: 16K L2 cache: 1024K L3 cache: 16384K NUMA node0 CPU(s): 0-15 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 lm constant_tsc pebs bts nopl cpuid pni dtes64 monitor ds_cpl vmx est tm2 cid cx16 xtpr pdcm lahf_lm pti tpr_shadow vnmi I hope that is enough information to be helpful. Thanks, Patrice -- System Information: Debian Release: 10.3 APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'stable-debug'), (500, 'stable') Architecture: amd64 (x86_64) Kernel: Linux 4.19.0-5-amd64 (SMP w/16 CPU cores) Locale: LANG=C, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages ncbi-blast+ depends on: ii libbz2-1.0 1.0.6-9.2~deb10u1 ii libc6 2.28-10 ii libgcc1 1:8.3.0-6 ii libgomp1 8.3.0-6 ii liblmdb0 0.9.22-1 ii libmbedcrypto3 2.16.0-1 ii libmbedtls12 2.16.0-1 ii libpcre3 2:8.39-12 ii libstdc++6 8.3.0-6 ii ncbi-data 6.1.20170106+dfsg1-0+deb10u2 ii perl 5.28.1-6 ii python 2.7.16-1 ii zlib1g 1:1.2.11.dfsg-1 ncbi-blast+ recommends no packages. ncbi-blast+ suggests no packages. -- no debconf information
