The MAF file sizes are unstable in the AnchorWave ProAli genome alignment results

[jiaanqiang]

Hi, Dr. Song Thank you for the development of the software anchorwav！But when I use it for comparison, I found that the generated MAF file results are incomplete. The results are sometimes complete for two genomes, but incomplete at other times. The error is as follows:

anchorwave_avx512: /opt/conda/conda-bld/anchorwave_1696951504789/work/src/impl/deNovoGenomeVariantCallingMultipleThreads.cpp:193: void genomeAlignmentSingleThread(std::vector, bool, bool, std::ofstream&, std::ofstream&, std::map<std::cxx11::basic_string, std::tuple<std::cxx11::basic_string<char, std::char_traits, std::allocator >, long int, long int, int> >&, std::map<std::cxx11::basic_string, std::tuple<std::cxx11::basic_string<char, std::char_traits, std::allocator >, long int, long int, int> >&, int, std::string, std::string, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, std::atomic_int&): Assertion `temp.compare(queryGenomeSequence) == 0' failed. /share/home/yzbsl_jiaaq/.conda/envs/AnchorWave/bin/anchorwave: line 22: 7689 Aborted (core dumped) "${EXE}_avx512" "$@" AVX512 is enabled.

If the results are unstable, it becomes challenging for me to determine which instance of the results is reliable. How can I resolve this issue? I appreciate your response. Thank you.

Anqiang Jia

[baoxingsong]

Please give -f a file name that does not exist or delete the old one each time before running AnchorWave. If that still does not work, please share your inputs and all the commands.

[jiaanqiang]

Thank you. I attempted to modify the output name in the MAF file, and indeed, it is now complete.