proali Error:deNovoGenomeVariantCallingMultipleThreads.cpp:204
chaimol opened this issue · 4 comments
Error code: Exited with exit code 134.
Error info :
anchorwave: /share/home/zhangsan/software/AnchorWave/AnchorWave/src/impl/deNovoGenomeVariantCallingMultipleThreads.cpp:204: void genomeAlignmentSingleThread(std::vector<AlignmentMatch>, bool, bool, std::ofstream&, std::ofstream&, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, std::__cxx11::string, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, std::atomic_int&, std::map<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >): Assertion `temp.compare(queryGenomerSequence)==0' failed.
A1_A2.bash: line 34: 347874 Aborted (core dumped)
I am use anchorwave v1.0.1 AVX512 is enabled
my running script is
anchorwave proali -i ${ref_gff} -as ${ref_abbr}.cds.fa -r ${ref_genome} -a ${query_abbr}.sam -ar ${ref_abbr}.sam -s ${query_genome} -n ${ref_abbr}_${query_abbr}.anchors -R 1 -Q 2 -t 4 -o ${ref_abbr}_${query_abbr}.alignment.maf -f ${ref_abbr}_${query_abbr}.alignment.f.maf
And the output file XXX.alignment.maf have been correct output of 29 lines, and then the above error occurs.
I allocated 230G memory and 4 cpus to this script.
Thanks for trying AnchorWanve. Could you provide enough information, so that I could repeat this error, please?
Including input data, every command, minimap2 version, etc.
I regenerated the sam file and ran it again afterwards. The program runs successfully, which may be caused by the incomplete sam file generated when I run it for the first time.
Hi,Baoxing Song,
I got the above error again core dumped.I used 4 cpus to allocate 230G of memory to the program at the same time, but the program still reported an error. I queried that the error was caused by insufficient memory allocated to C++.
What I want to ask is, do you have any plans to support the continued analysis of breakpoints, such as this interruption caused by insufficient memory, can you support proali to continue the analysis in the future? You know it takes a long time to rerun proali every time.
Thanks. This is a good suggestion. I will try to implement this feature.