tak-gk
commented
1 year ago I found my fault relating to this issue. This issue was caused by the overuse of RAM because of a blank fasta sequence in the input file like below.
blank
seq1 ATGC... seq2 ATGC...
Thank you very much.
epruesse
I am using the SINA 1.7.2 for aligning and searching taxonomy of fasta sequences (550bp, about 5000 sequences). However the processes always terminated with getting the 'Signal 11' error. Even the similar analyses were tried on Ubuntu 22.04 installed on different platforms (intel iMac RAM=64GB & Workstaion RAM=198GB), I got the same error and termination.
I have tried disc and RAM check (fsck, memtest86+) but I got no solution for this issue.
Could you please give some advices and solutions for me.
Thank you very much.
----- Input command -----
$ sina -i clustered.fasta -o otu99_alsina.fas --meta-fmt csv --threads 4 --db /home/USER/local/share/db/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb --fs-kmer-len 10 --search --search-min-sim 0.70 --lca-fields tax_slv
----- Obtained messages -----
16:27:19 [SINA] This is SINA 1.7.2. 16:27:25 [famfinder] Using internal engine for reference search 16:27:25 [SINA] Aligner ready. Processing sequences Processing: 16% |██████████▍ | 720/4630 [00:00:36 / 00:03:17]
-------------------- ARB-backtrace 'received signal 11': /home/USER/miniforge3/envs/sina17/bin/../lib/arb/lib/libCORE.so(GBK_dump_backtrace(_IO_FILE, char const)+0x36)[0x7f03567d80e6] /home/USER/miniforge3/envs/sina17/bin/../lib/arb/lib/libCORE.so(+0xf237)[0x7f03567da237] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f0356242520] /home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::cseq_comparator::operator()(sina::annotated_cseq const&, sina::annotated_cseq const&)+0x10c)[0x7f0356a3c50c] /home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(+0x94112)[0x7f0356a42112] /home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::famfinder::impl::match(std::vector<sina::search::result_item, std::allocator >&, sina::annotated_cseq const&)+0x524)[0x7f0356a435a4]
/home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::famfinder::impl::operator()(sina::tray)+0x1508)[0x7f0356a49108]
/home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::famfinder::operator()(sina::tray const&)+0x42)[0x7f0356a49ad2]
sina(+0x20dc2)[0x555dce557dc2]
sina(+0x5389c)[0x555dce58a89c]
sina(+0x539a1)[0x555dce58a9a1]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x21455)[0x7f03568fa455]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x2175d)[0x7f03568fa75d]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(tbb::interface7::internal::task_arena_base::internal_execute(tbb::interface7::internal::delegate_base&) const+0xf4)[0x7f03568f6154]
sina(+0x498df)[0x555dce5808df]
sina(+0x1e1b5)[0x555dce5551b5]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f0356229d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f0356229e40]
sina(+0x1e59d)[0x555dce55559d]
-------------------- End of backtrace
16:27:55 [ARB I/O] Closing ARB database '"/home/USER/local/share/db/SILVA_138.1_SSURef_NR99_12_06_20_opt.arb"' ...
Processing: 16% |██████████▍ | 720/4630 [00:00:36 / 00:03:17]
-------------------- ARB-backtrace 'received signal 11': /home/USER/miniforge3/envs/sina17/bin/../lib/arb/lib/libCORE.so(GBK_dump_backtrace(_IO_FILE, char const)+0x36)[0x7f03567d80e6] /home/USER/miniforge3/envs/sina17/bin/../lib/arb/lib/libCORE.so(+0xf237)[0x7f03567da237] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f0356242520] /home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::query_arb::getCseqUncached(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)+0x54)[0x7f0356a5b614]
/home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::query_arb::getCseq(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)+0x9b)[0x7f0356a5b85b]
/home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::kmer_search::impl::find(sina::annotated_cseq const&, std::vector<sina::search::result_item, std::allocator >&, unsigned int)+0x5f7)[0x7f0356aa8cf7]
/home/USER/miniforge3/envs/sina17/bin/../lib/libsina.so.0(sina::search_filter::operator()(sina::tray)+0xf1)[0x7f0356aa16c1]
sina(+0x20cc3)[0x555dce557cc3]
sina(+0x5389c)[0x555dce58a89c]
sina(+0x539a1)[0x555dce58a9a1]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x21455)[0x7f03568fa455]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x2175d)[0x7f03568fa75d]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x1bb07)[0x7f03568f4b07]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x1a0f1)[0x7f03568f30f1]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x1679c)[0x7f03568ef79c]
/home/USER/miniforge3/envs/sina17/bin/../lib/libtbb.so.2(+0x169aa)[0x7f03568ef9aa]
/lib/x86_64-linux-gnu/libc.so.6(+0x94b43)[0x7f0356294b43]
/lib/x86_64-linux-gnu/libc.so.6(+0x126a00)[0x7f0356326a00]
-------------------- End of backtrace
[Terminating with signal 11]