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  • MAKER Exonerate Error

    Hello,

    I am currently running MAKER version 2.31.8 using MPI but I keep getting the following error when running Exonerate:

    Maker command used: mpiexec -mca btl ^openib -n 16 maker

    ** (process:18773): WARNING **: Compiled with assertion checking - will run slowly
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18771 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/9/gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.for.21933-23968
    ** (process:18775): WARNING **: Compiled with assertion checking - will run slowly
    .9.fasta -t /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.p.exonerate
    **
    Do you know a workaround this problem? I would really appreciate your help.

    maker log:

    polishing proteins
    polishing proteins
    running exonerate search.
    #--------- command -------------#
    Widget::exonerate:rotein2genome:
    /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/2/ATMG00830%2E1.for.22122-24034.2.fasta -t /media/raid/tmp/maker_DYrlgS/2/13225915.22122-24034.2.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/2/13225915.22122-24034.ATMG00830%2E1.p.exonerate
    #-------------------------------#
    polishing proteins

    ** (process:18769): WARNING **: Compiled with assertion checking - will run slowly
    running exonerate search.
    #--------- command -------------#
    Widget::exonerate:rotein2genome:
    /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/9/gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.for.21933-23968.9.fasta -t /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.p.exonerate
    #-------------------------------#
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18769 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/2/ATMG00830%2E1.for.22122-24034.2.fasta -t /media/raid/tmp/maker_DYrlgS/2/13225915.22122-24034.2.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/2/13225915.22122-24034.ATMG00830%2E1.p.exonerate

    ** (process:18771): WARNING **: Compiled with assertion checking - will run slowly
    running exonerate search.
    #--------- command -------------#
    Widget::exonerate:rotein2genome:
    /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/7/ATMG00960%2E1.for.21510-22918.7.fasta -t /media/raid/tmp/maker_DYrlgS/7/13225915.21510-22918.7.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/7/13225915.21510-22918.ATMG00960%2E1.p.exonerate
    #-------------------------------#

    ** (process:18773): WARNING **: Compiled with assertion checking - will run slowly
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18771 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/9/gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.for.21933-23968
    ** (process:18775): WARNING **: Compiled with assertion checking - will run slowly
    .9.fasta -t /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.p.exonerate
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18773 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/2/ATMG00830%2E1.for.22122-24034.2.fasta -t /media/raid/tmp/maker_DYrlgS/2/13225915.22122-24034.2.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/2/13225915.22122-24034.ATMG00830%2E1.p.exonerate
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18775 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/7/ATMG00960%2E1.for.21510-22918.7.fasta -t /media/raid/tmp/maker_DYrlgS/7/13225915.21510-22918.7.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/7/13225915.21510-22918.ATMG00960%2E1.p.exonerate

    ** (process:18777): WARNING **: Compiled with assertion checking - will run slowly

    ** (process:18779): WARNING **: Compiled with assertion checking - will run slowly
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18779 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/7/ATMG00960%2E1.for.21510-22918.7.fasta -t /media/raid/tmp/maker_DYrlgS/7/13225915.21510-22918.7.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/7/13225915.21510-22918.ATMG00960%2E1.p.exonerate
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18777 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/9/gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.for.21933-23968.9.fasta -t /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/9/13225915.21933-23968.gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.p.exonerate
    ERROR: Exonerate failed
    --> rank=2, hostname=lettucelab.cpp.edu
    ERROR: Failed while polishing proteins
    ERROR: Chunk failed at level:10, tier_type:3
    polishing proteins
    running exonerate search.
    #--------- command -------------#
    Widget::exonerate:rotein2genome:
    /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/9/AT2G07768%2E1.for.21510-22681.9.fasta -t /media/raid/tmp/maker_DYrlgS/9/13225915.21510-22681.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/9/13225915.21510-22681.AT2G07768%2E1.p.exonerate
    #-------------------------------#
    FAILED CONTIG:13225915


    ** (process:18785): WARNING **: Compiled with assertion checking - will run slowly
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18785 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/9/AT2G07768%2E1.for.21510-22681.9.fasta -t /media/raid/tmp/maker_DYrlgS/9/13225915.21510-22681.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/9/13225915.21510-22681.AT2G07768%2E1.p.exonerate

    ** (process:18787): WARNING **: Compiled with assertion checking - will run slowly
    **
    ERRORrotein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)
    sh: line 1: 18787 Aborted /usr/bin/exonerate -q /media/raid/tmp/maker_DYrlgS/9/AT2G07768%2E1.for.21510-22681.9.fasta -t /media/raid/tmp/maker_DYrlgS/9/13225915.21510-22681.9.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /media/raid/tmp/maker_DYrlgS/9/13225915.21510-22681.AT2G07768%2E1.p.exonerate
    ERROR: Exonerate failed
    --> rank=9, hostname=lettucelab.cpp.edu
    ERROR: Failed while polishing proteins
    ERROR: Chunk failed at level:10, tier_type:3
    ERROR: Chunk failed at level:4, tier_type:0
    FAILED CONTIG:13225915

    examining contents of the fasta file and run log



    --Next Contig--

    Processing run.log file...
    MAKER WARNING: The file 10gerk62.maker.output/10gerk62_datastore/17/53/13225915//theVoid.13225915/0/13225915.22122-24034.ATMG00830%2E1.p_exonerate
    did not finish on the last run and must be erased
    MAKER WARNING: The file 10gerk62.maker.output/10gerk62_datastore/17/53/13225915//theVoid.13225915/0/13225915.21510-22681.AT2G07768%2E1.p_exonerate
    did not finish on the last run and must be erased
    MAKER WARNING: The file 10gerk62.maker.output/10gerk62_datastore/17/53/13225915//theVoid.13225915/0/13225915.21510-22918.ATMG00960%2E1.p_exonerate
    did not finish on the last run and must be erased
    MAKER WARNING: The file 10gerk62.maker.output/10gerk62_datastore/17/53/13225915//theVoid.13225915/0/13225915.21933-23968.gi%7C565342117%7Cref%7CXP_006338208%2E1%7C.p_exonerate
    did not finish on the last run and must be erased

  • #2
    Sorry for the old post revival, but I also had the same problem so solution below in case it helps someone:

    ERROR: protein2genome.c:25:Protein2Genome_Data_create: assertion failed: (target->alphabet->type == Alphabet_Type_DNA)

    System data:
    SELinux, 4.16.9-200.fc27.x86_64

    With exonerate built using: sudo dnf install exonerate

    exonerate from exonerate version 2.4.0
    Using glib version 2.53.4
    Built on Aug 2 2017


    To solve this I needed to sudo dnf remove exonerate, then downloaded the pre-compiled binary, as described in https://github.com/mossmatters/HybPiper/issues/10.

    I re-built Maker again before testing successfully, and ctl files for any projects also need to be recreated.

    The problem seems to be that the --disable-assert flag is set to false on the current exonerate install instead of true. There's probably a smarter way to fix this, but this method works for me.

    Cheers,
    Andrew
    Last edited by andrewlandels; 06-19-2018, 01:10 AM. Reason: Removed smiley face from "ERROR:protein2genome", got true and flase the wrong way around...

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