SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
MAKER prerequisites and dependencies NYGen Bioinformatics 0 07-11-2015 06:39 PM
maker weird thing yzzhang Bioinformatics 1 03-06-2013 06:49 AM
Maker polijana Bioinformatics 3 02-10-2013 06:21 PM
Help with Exonerate output mycorr10 Bioinformatics 0 02-06-2012 02:50 PM
Genemark-ES and Maker Rockx Bioinformatics 0 12-18-2011 07:17 PM

Reply
 
Thread Tools
Old 09-01-2016, 05:53 PM   #1
milo0615
Member
 
Location: Walnut, California

Join Date: Dec 2012
Posts: 39
Default 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
milo0615 is offline   Reply With Quote
Old 06-19-2018, 02:08 AM   #2
andrewlandels
Junior Member
 
Location: UK

Join Date: Jun 2018
Posts: 1
Default

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 at 02:10 AM. Reason: Removed smiley face from "ERROR:protein2genome", got true and flase the wrong way around...
andrewlandels is offline   Reply With Quote
Reply

Tags
exonerate, maker, mpiexec, protein2genome

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 10:09 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO