egapx:setup_genome:get_genome_info terminated with an error exit status (3)

[Johnsonzcode]

Hi developers

When I ran egapx with singularity and docker, it turned out the same error.

Critical: (CCoreException::eNullPtr) Attempt to access NULL pointer.
     Stack trace:
      /img/dev/gp/arch/x86_64/lib/libxncbi.so /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/src/corelib/ncbiobj.cpp:1012 ncbi::CObject::ThrowNullPointerException() offset=0x0 addr=0x7f5b58f69a11
       /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/include/corelib/ncbiobj.hpp:1051 ThrowNullPointerException offset=0x0 addr=(nil)
       /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/include/objmgr/tse_handle.hpp:682 GetNonNullPointer offset=0x0 addr=(nil)
       /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/src/objmgr/bioseq_handle.cpp:119 operator-> offset=0x0 addr=(nil)
      /img/dev/gp/arch/x86_64/lib/libxobjmgr.so /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/include/corelib/ncbiobj.hpp:830 ncbi::objects::CBioseq_Handle::x_GetInfo() const offset=0x0 addr=0x7f5b5edfb2c8
      /img/dev/gp/arch/x86_64/lib/libxobjmgr.so /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/src/objmgr/bioseq_handle.cpp:173 ncbi::objects::CBioseq_Handle::GetId() const offset=0x0 addr=0x7f5b5edfb3f8
      /img/dev/gp/arch/x86_64/bin/gc_create /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/src/internal/gpipe/app/common/gc_create.cpp:326 CGcCreateApp::Run() offset=0x0 addr=0x40fa68
      /img/dev/gp/arch/x86_64/lib/libxncbi.so /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/src/corelib/ncbiapp.cpp:686 ncbi::CNcbiApplicationAPI::x_TryMain(ncbi::EAppDiagStream, char const*, int*, bool*) offset=0x0 addr=0x7f5b58eb4cba
      /img/dev/gp/arch/x86_64/lib/libxncbi.so /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/src/corelib/ncbiapp.cpp:1024 ncbi::CNcbiApplicationAPI::AppMain(int, char const* const*, char co
nst* const*, ncbi::EAppDiagStream, char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) offset=0x0 addr=0x7f5b58eb73b4
      /img/dev/gp/arch/x86_64/bin/gc_create /export/home/gpipe/TeamCity/Agent2/work/c27a3979e6cc6283/ncbi_cxx/src/internal/gpipe/app/common/gc_create.cpp:496 main offset=0x0 addr=0x40a54d
      /usr/lib/x86_64-linux-gnu/libc-2.31.so :0  offset=0x0 addr=0x7f5b5651c082
      /img/dev/gp/arch/x86_64/bin/gc_create :0  offset=0x0 addr=0x40a6ad
       :0  offset=0x0 addr=0xffffffffffffffff

Critical: (106.16) Application's execution failed (CCoreException::eNullPtr) Attempt to access NULL pointer.

Do you know how I could solve it?

Best wish
Johnson

[boukn]

Can you link your fasta genome input file?

[Johnsonzcode]

I am annotating the pan sequence, it is quite fragmented. It looks like:

>k141_294784 flag=0 multi=1.0000 len=590
GGAAGGAAAGAAAGGAGAAAGAAGGAAAGAAGGAAAGAAAGAAGGAAAGAAGGAAAGAAAGAAGGAAAGAAGGAAAGAAAGAAGGAAAGAAGGAAAGAAAGAAGGAAAGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAGAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAGAAAGAAAGAAAGAAAGAAAGAAA
>k141_336896 flag=1 multi=2.0000 len=508
CTTCGCATACAGAGACCTCAACATGAGTTCTGACTATATGACATCCTTCAAGGCAACTTAGGGATGAGGGTAGAATTGTGACACGTGGAGATGCATGTGGTGACCAAAGGTGAAAACAAACACCTTCCAAAGTGGATTACAGGGTGATTCTTTACCTTTCCACTAGTGGAGTACGCAGGTGCTGTCAGCACAAGGTGCCAGGGGCTGTGAAGCACTGCTGCTTTACTGCATCGCTTCTTTAAGACCCACAATACCTTCTACATCTCGAGCCCGCTATCACACAGTGCTTAAAGGCTCACTACTGGTTACACTCACTGATTTATTTTGTAAACAAAGAGATCCGTAAACAAAGGGATTTACAAACAGTAACACGACTATATCGTTTCCATAACTTTCAGTTCCCACAGACATCATCTTTACCCCAGCTTAACGGCCCTGCAGCGCTGGGAACAGAGCACAGGCCAAATTAACCCAAGGGAATTCAACAACAACAACAAATAAATAACCC
>k141_57904 flag=1 multi=2.0000 len=564
GCCAGAGTAACATCTGGTTCTGCAGCTGACACTGTTCTTGGAGGAGTGAAGATCGGAGCTAGGCTTTCATGGTCACGACCAGGAAAACGTACCCCTCTGGATCTCAAACTCTTGTAAGTCTCTTCATACACAGGTAAATAGCGAAGCTCACTCGATGATTCTCCCCAAGCTTCAATTAACACCAGGGCCTTGTTCCGATTGTTAACAACAGTTTGAGGGTCATCAATCAACTTCACCATCTCATCCAGAACCCTCTCAGCAGCAATTTCGGAGAACGCCTTCTCGCAATTCTTTGCAATAGTTTCAAGTAACACCAACCCTAAGTACTGAATCCTGGGGCTCTTCAGCATTATCCTTTTCTTCACGCCCCTAATCAGTTCAACACTATTGATTCTATCGTGATTAATCATGTCACAAAGCTCAAGATTCATAGCCCAATCAGGTTCATCCAGAGTTTCAGCTGTGGCTTCCTCGACAAGCTTATCAGCCTGATTTGGGCCTTGGAAAAGTTCCTTCATCTTGAAACTCATCGAGCTCATTCCAGCAGTGATCTTTTGCCCAACC
>k141_342160 flag=1 multi=39.0000 len=785
TCAGCACTATTTCAAAAAAAGCATTTTATTCTTATTCTGAAATTAAAATAACATTTCTTAGCATTAAAAAAATCATAAAAGGAACAAATTTATCTGCTTTAAATAGCACTTTTATAAGTAGAAGGAGCCACAGATATATATGTTTACTTGAATTATTTATTTTATATTTTCCTTTCAGATTTGGAGATAGTTCCATACTTTTAGTTCTCTTACGGTTTTTTAAATTTTAGTTTACAGGCAGCATTAAGAGCAGACCCAAAGGACTTCAATTGTTGGGAATCGTTAGGAGAAGCATACTTAAGCAGAGGAGGCTACACAACAGCCTTGAAGTCCTTCACAAAAGCCAGTGAGCTGAACCCAGAATCCATATACAGTGTGTTTAAGGTTGCAGCAATACAGCAAATCCTAGGCAAATATAAGGAGGCTGTAGCTCAATACCAGATGATCATTAAAAAGAAAGAAGATTATGTGCCTGCTTTAAAAGGTAATTTATTTTTAGTAGCTCCTTTGACTTTTATGATCCTGAAGTATAAAATCCTTGAGTAGATTTCCTGCCTAAATGTATTGAATAACTTGAAAAGGACTTCTTTAGTCAACAGCAAGCATCCATATGAACCTCTTACAGTATAGCTTATATAAATTTGAATATAAAAAGATCAAATCTTGTTTCACAAGTTAATAAATAGTAATGTGACAGAGATTTAACTTTTAGACAAACAGTATGATAACTATTAGATCTAAAAATTGATCTCTAAAACATGTTTCCCTACTCTTACATTTTGATA
>k141_610574 flag=1 multi=5.0000 len=841
GTCAGGTCTGGTCCTTCTCACTTCCTGTCCTGTGTCCTATAATGAATGTGGTCTTCATCACCTTTTTAATAATAGCTCTCATTGCCTCAAAAGAATGTTGCATATTCCTATAGTACTTCTATAGTCTGCCTGAACTCATCATCAACTTTCTCCCTTCCAGATGATGCCACCAGTCCCCATTTCTCAACACGTCATGAAGGGTCCTTCCAAGTTCCTGTCCTGTGTGCTGTAATGAATGTGGTCTTCATCACCATTTTAATCATAGCTCTCATTGCCTTATCAGTGGGCCAATACAATTGTCCAGGCCAATACACATTCTCAATGCCATCAGACAGCCATGTTTCTTCATGCTCTGAGGACTGGGTTGGCTACCAGAGGAAATGCTACTTTATTTCTACTGTGAAGAGGAGCTGGACTTCAGCCCAAAATGCTTGTTCTGAACATGGTGCTACTCTTGCTGTCATTGATTCTGAAAAGGACATGAACTTTCTAAAACGATACGCAGGTAGAGAGGAACACTGGGTTGGACTGAAAAAGGAACCTGGTCACCCATGGAAGTGGTCAAATGGCAAAGAATTTAACAACTGGTAAGTCTCCAGAAGTCTCTTTATATTCCCCAGGGTGGCATCTCAGGAAAATCACTTTCCTTTTCTCCTTTCAAAGCACTTTAAATATAAAGGCTGAGCTCTTCAAGAGCTCTAACAATCTCTTCTGAATGCGTATACTCTGGAATTCTTTAATAACAGGCTTTATTATTATTCTTTTTCTTTATCCACACTTATAATACATAAAATAAATGCTTATAGTAATTTTTCTCAGCAAACTCTAATGTGAGTAGTAG
>k141_431632 flag=1 multi=2.0000 len=633
TACCGCGTGGGATAAAAATCCGGCCAGTATGGCTAACCTTGAGCGTATTAAAGCGGCAGAAGGGCTGGATAATCTGCAAACCGACATTGTCGATCTGAATACATTGACCTTTGACGGCGAGTACGATTTTATTCTCTCGACGGTGGTTATGATGTTTCTTGAGGCGCAAACCATTCCCAGTTTCATTGCCAATATGCAACGCTGCACAAAACCCGGCGGGTATAATTTGATTGTTGCGGCAATGGATACGCCGGACTTTCCCTGTACGGTGGGATTCCCGTTCGCTTTTAAAGAAGGCGAATTACGCCGCTATTACGAAGGATGGGACATGCTGAAATACAACGAAGATGTCGGCGAGCTTCACCGCACGGACGAAAACGGCAACCGTATCAAACTGCGCTTTGCTACGATGCTGGCGAGAAAAACGGCCTGAGCGATGCAAGTTCTGTAAGTCTCGCTGCGTTCGGCATTTTTTTGTCGGGCGCTGCGTTCAAATTGTGCTGTCGTTACCATTTTTAGTGCATCCAGAATGATTTCGTTTTGCTATTATTTCCTTTGCATCATTGCGAAGACTAAAGGGATCGTTTCATGCGTACTCATACTTTATTTAAAGTTGCAGTGCTTACTGGCTTG