MAKER Exonerate Error

[milo0615]

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

[andrewlandels]

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