nathanweeks / exonerate Goto Github PK

Hi Nathan,

are you aware of this forked repo?

https://github.com/hotdogee/exonerate-gff3 which is an improved version of exonerate-2.2.0 with GFF3 format output support

Maybe you could unite the efforts.

Some patches and compile/install tricks can be inferred from the ebuild
https://data.gpo.zugaina.org/science/sci-biology/exonerate-gff3
https://cgit.gentoo.org/proj/sci.git/tree/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch?id=d209b24ac3b9de78f7048fb76467c42bad604263 # well this patch chnages the part you commented out but

There is also an on-top utility https://github.com/lufuhao/ExonerateTransferAnnotation .

There is a similar utility https://cgit.gentoo.org/proj/sci.git/commit/sci-biology/ESTate/ESTate-0.5.ebuild?id=4c181b3959260dbe65d3801005b99f1a6e4db33c

Hello. I'm trying to run the latest release version of exonerate while some of my query sequences contain selenocysteine (U). The tool was compiled with no custom configuration flags on the latest Ubuntu release. I'm getting this error.

** FATAL ERROR **: Unknown amino acid [U]
exiting ...

The command I used to start the process

nohup exonerate -q prot/* -t gen/* -Q protein -T dna -m protein2genome --percent 50 --showtargetgff -n 1 --maxintron 50000 --cores 1 > out.gff &

Here are the faulty sequences from the prot directory

cat prot/*.fna | grep -v -e "^>" | grep "U"

MVYISNGQVLDSRSQSPWRLSLITDFFWGIAEFVVLFFKTLLQQDVKKRRSYGNSSDSRYDDGRGPPGNPPRRMGRINHLRGPSPPPMAGGUGR
MAEASATGACGEAMAAAEGSSGPAGLTLGRSFSNYRPFEPQALGLSPSWRLTGFSGMKGUGCKVPQEALLKLLAGLTRPDVRPPLGRGLVGGQEEASQEAGLPAGAGPSPTFPALGIGMDSCVIPLRHGGLSLVQTTDFFYPLVEDPYMMGRIACANVLSDLYAMGITECDNMLMLLSVSQSMSEEEREKVTPLMVKGFRDAAEEGGTAVTGGQTVVNPWIIIGGVATVVCQPNEFIMPDSAVVGDVLVLTKPLGTQVAVNAHQWLDNPERWNKVKMVVSREEVELAYQEAMFNMATLNRTAAGLMHTFNAHAATDITGFGILGHSQNLAKQQRNEVSFVIHNLPIIAKMAAVSKASGRFGLLQGTSAETSGGLLICLPREQAARFCSEIKSSKYGEGHQAWIVGIVEKGNRTARIIDKPRVIEVLPRGATAAVLAPDSSNASSEPSS
MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG

Best Regards

When "--showalignment yes" I continually get "** FATAL ERROR **: Unknown amino acid [-]". When "--showalignment no" it's fine. Is this a problem with the gap symbol?
Thanks

I'm trying to compile Exonerate, but I got this error. I'm a bit lost.

gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I.  -DCUSTOM_GUINT64_FORMAT="\"lu\""    -g -O2 -I../..//scratch/c7701100/apps/glib-2.10.0 -I../..//scratch/c7701100/apps/glib-2.10.0/. -I../..//scratch/c7701100/apps/glib-2.10.0/./glib   -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c
In file included from fsm.test.c:17:
fsm.h:24:37: error: glib.h: No such file or directory
In file included from fsm.h:25,
                 from fsm.test.c:17:
recyclebin.h:30: error: expected specifier-qualifier-list before ‘gint’
recyclebin.h:40: error: expected ‘)’ before ‘*’ token
recyclebin.h:45: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RecycleBin_memory_usage’
recyclebin.h:47: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RecycleBin_alloc’
recyclebin.h:48: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘RecycleBin_alloc_blank’
recyclebin.h:49: error: expected declaration specifiers or ‘...’ before ‘gpointer’
In file included from fsm.test.c:17:
fsm.h:33: error: expected specifier-qualifier-list before ‘gpointer’
fsm.h:36: error: expected declaration specifiers or ‘...’ before ‘*’ token
fsm.h:36: error: expected ‘)’ before ‘a’
fsm.h:40: error: expected specifier-qualifier-list before ‘guchar’
fsm.h:56: error: expected ‘)’ before ‘*’ token
fsm.h:58: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘FSM_memory_usage’
fsm.h:62: error: expected ‘)’ before ‘data’
fsm.h:63: error: expected declaration specifiers or ‘...’ before ‘FSM_Destroy_Func’
fsm.h:64: error: expected declaration specifiers or ‘...’ before ‘gpointer’
fsm.h:66: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘FSM_add’
fsm.h:69: error: expected ‘)’ before ‘seq_pos’
fsm.h:73: error: expected declaration specifiers or ‘...’ before ‘gchar’
fsm.h:73: error: expected declaration specifiers or ‘...’ before ‘FSM_Traverse_Func’
fsm.h:74: error: expected declaration specifiers or ‘...’ before ‘gpointer’
fsm.h:76: error: expected declaration specifiers or ‘...’ before ‘guchar’
fsm.h:77: error: expected declaration specifiers or ‘...’ before ‘guchar’
fsm.test.c:19: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘test_merge_Func’
fsm.test.c:28: error: expected ‘)’ before ‘seq_pos’
fsm.test.c: In function ‘main’:
fsm.test.c:38: error: ‘gint’ undeclared (first use in this function)
fsm.test.c:38: error: (Each undeclared identifier is reported only once
fsm.test.c:38: error: for each function it appears in.)
fsm.test.c:38: error: expected ‘;’ before ‘count’
fsm.test.c:40: error: ‘test_merge_Func’ undeclared (first use in this function)
fsm.test.c:53: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘i’
fsm.test.c:53: error: ‘i’ undeclared (first use in this function)
fsm.test.c:54: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘*’ token
fsm.test.c:54: error: ‘tolower_filter’ undeclared (first use in this function)
fsm.test.c:54: error: ‘guchar’ undeclared (first use in this function)
fsm.test.c:54: error: expected expression before ‘)’ token
fsm.test.c:62: error: too many arguments to function ‘FSM_add_traversal_filter’
fsm.test.c:63: error: ‘test_traverse_Func’ undeclared (first use in this function)
fsm.test.c:63: error: ‘count’ undeclared (first use in this function)
fsm.test.c:63: error: too many arguments to function ‘FSM_traverse’
make[2]: *** [fsm.test.o] Error 1
make[2]: Leaving directory `/gpfs/scratch/c7701100/apps/exonerate/src/struct'
make[1]: *** [install-recursive] Error 1
make[1]: Leaving directory `/gpfs/scratch/c7701100/apps/exonerate/src'
make: *** [install-recursive] Error 1

Thank you
F

Using:

$ exonerate --version
exonerate from exonerate version 2.2.0
Using glib version 2.22.5
Built on Jun 26 2012
Branch: unnamed branch

Running as follows gives a segmentation fault:

$ exonerate -m affine:local --bestn 5 --ryo "INFO: %qi %qal %pi %tS %ti\n" testc.fasta  19041.allrefs.fasta
Command line: [exonerate -m affine:local --bestn 5 --ryo INFO: %qi %qal %pi %tS %ti\n testc.fasta 19041.allrefs.fasta]
Hostname: [localhost]
Segmentation fault

running gdb:

$ gdb exonerate
(gdb) run -m affine:local --bestn 5 --ryo "INFO: %qi %qal %pi %tS %ti\n" testc.fasta 19041.allrefs.fasta
Starting program: exonerate -m affine:local --bestn 5 --ryo "INFO: %qi %qal %pi %tS %ti\n" testc.fasta 19041.allrefs.fasta
[Thread debugging using libthread_db enabled]
Command line: [exonerate -m affine:local --bestn 5 --ryo INFO: %qi %qal %pi %tS %ti\n testc.fasta 19041.allrefs.fasta]
Hostname: [localhost]

Program received signal SIGSEGV, Segmentation fault.
0x00000000004081bb in Scheduler_Cell_init (row=0x12627b0, spair=0x1260900, seed=0x7fffffffc5b0) at ../../src/sdp/scheduler.c:714
714             cell->traceback[i] = NULL;
Missing separate debuginfos, use: debuginfo-install sssd-client-1.9.2-82.4.el6_4.x86_64

gdb with core dump:

$ gdb exonerate core.28189 
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-60.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from exonerate...done.
¡New Thread 28189¿
Missing separate debuginfo for 
Try: yum --disablerepo='*' --enablerepo='*-debug*' install /usr/lib/debug/.build-id/6e/08187df14a79463ec23c6260b6e3e0620a2f6a
Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done.
¡Thread debugging using libthread_db enabled¿
Loaded symbols for /lib64/libpthread.so.0
Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libm.so.6
Reading symbols from /lib64/libglib-2.0.so.0...(no debugging symbols found)...done.
Loaded symbols for /lib64/libglib-2.0.so.0
Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libc.so.6
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Reading symbols from /lib64/libnss_files.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_files.so.2
Reading symbols from /lib64/libnss_sss.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libnss_sss.so.2
Core was generated by `exonerate -m affine:local --bestn 5 --ryo'.
Program terminated with signal 11, Segmentation fault.
£0  0x00000000004081bb in Scheduler_Cell_init (row=0x270f7b0, spair=0x270d900, seed=0x7fffec9481f0) at ../../src/sdp/scheduler.c:714
714             cell->traceback¡i¿ = NULL;
Missing separate debuginfos, use: debuginfo-install glib2-2.26.1-3.el6.x86_64 glibc-2.12-1.132.el6.x86_64 sssd-client-1.9.2-82.4.el6_4.x86_64

Something is causing i to extend outside the bounds of the array at cell->traceback[i] = NULL;? Not had much chance to debug properly!

Strangely running the binary is fine? Something to do with new glib version in the compiled from source version above perhaps?

$ ~/exonerate-2.2.0-x86_64/bin/exonerate --version
exonerate from exonerate version 2.2.0
Using glib version 2.4.7
Built on Oct 17 2008
Branch: unnamed branch

Hi, I want to use exonerate to predict gene. but the result don't show the exon phase and result premature termination of the gene.here is my code

exonerate -t genome.fa -q query.fa --model protein2genome --bestn 1 --showtargetgff > exonerate.txt

and here is my partal result:

GWHACEC00000010 exonerate:protein2genome:local gene 47782722 47802710 5777 + . ID=0;Name=0;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local CDS 47782722 47782829 . + . ID=.;Name=.;Alias=.;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local exon 47782722 47782829 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice5 47782830 47782831 . + . ID=1;Name=1;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local intron 47782830 47785356 . + . ID=1;Name=1;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice3 47785355 47785356 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local CDS 47785357 47785428 . + . ID=.;Name=.;Alias=.;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local exon 47785357 47785428 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice5 47785429 47785430 . + . ID=2;Name=2;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local intron 47785429 47785584 . + . ID=2;Name=2;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice3 47785583 47785584 . + . ID=1;Name=1;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local CDS 47785585 47785639 . + . ID=.;Name=.;Alias=.;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local exon 47785585 47785639 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice5 47785640 47785641 . + . ID=3;Name=3;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local intron 47785640 47785759 . + . ID=3;Name=3;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice3 47785758 47785759 . + . ID=2;Name=2;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local CDS 47785760 47785902 . + . ID=.;Name=.;Alias=.;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local exon 47785760 47785902 . + . ID=0;Name=0;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice5 47785903 47785904 . + . ID=4;Name=4;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local intron 47785903 47786085 . + . ID=4;Name=4;Alias=_E1;Parent=0;Target=.
GWHACEC00000010 exonerate:protein2genome:local splice3 47786084 47786085 . + . ID=3;Name=3;Alias=_E1;Parent=0;Target=.

could you tell how to add phase information at the eighth column , thank you very much.

Hello,
I've been trying to do affine:global alignment using exonerate v2.4.0 . I've tried this using both the conda package, and installing from source as described in the README. Both installation methods result in the same problem: when using the exhaustive search it never seems to end, even when fed extremely short sequences. The command I've been using is as follows:
/usr/local/bin/./exonerate -S FALSE -E TRUE --showalignment TRUE --showvulgar TRUE -V 9 --model affine:global -Q dna -T dna -q test3.fa -t test4.fa
As a test I tried aligning 5 bases to one another using this set of inputs, and it still had not finished running after two hours. The same problem for longer sequences.
The output from this set of inputs is the following:

Command line: [/usr/local/bin/./exonerate -S FALSE -E TRUE --showalignment TRUE --showvulgar TRUE -V 9 --model affine:global -Q dna -T dna -q test3.fa -t test4.fa]
Hostname: [Nathans-MacBook-Pro.local]
** Message: Creating analysis with query[DNA] target[DNA]
** Message: Load query for pairwise comparision [test3] (5)
** Message: Load target for pairwise comparison [test4] (5)
** Message: Load query for pairwise comparision [test3] (5)
** Message: Load target for pairwise comparison [test4] (5)

It never seems to get past the loading step. If I run --model affine:local without the -E flag it runs without a problem, but if I include the E flag it fails to finish running as well. It seems like the exhaustive search is never finishing for some reason, even when fed very short sequences.

Hi,
How can I get my protein sequence after I run exonerate --model est2genomeand get gff3 file?
Thanks,
sun,

Hi,

i am trying to run exonerate with --bestn 1 option, but there is no output produced outof it compared to if i did not put any of the --bestn option,
why is it happening?

my command line is here
/path/exonerate --model est2genome -q /path//Trans.fasta -t /path/genome.fa --bestn 1 --showtargetgff yes --score 1000 > exo_filt_532_a.out

please point to me where is the fault?

thanks

Does somebody try to use the options --geneticcode if I do:

exonerate --model protein2genome --showcigar T --useaatla F --showquerygff T --showtargetgff T --minintron 142 --maxintron 4000 --intronpenalty -35 --geneticcode 4 nad5 contig1

It totally ignore the fact I want use the genetic code 4 ... I obtain exactly the same result if I used the standard genetic code and it shouldn't be the case. Am I the only one with this issue ?

Hi,

I'm getting this segmentation fault, and I don't know how to fix it, any help?

Segmentation fault      exonerate --showsugar T --showtargetgff T --softmasktarget T -n 2 --model protein2genome --percent 50 --refine full --query $EXONINPUT.$SPLIT.fasta --target $TARGET

exonerate --version
exonerate from exonerate version 2.4.0
Using glib version 2.46.2
Built on Nov 22 2019

Best
F

Hi,

Automake 1.15 has known issues that didn't appear with older versions, but is the only version that comes through apt on Ubuntu 16.04. Exonerate generates an "unable to find aclocal" error on automake 1.15, but to work around this after cloning the git you need to manually run:
sudo aclocal
sudo automake
sudo make
You MAY need to run ./configure before that (I did, but didn't test without a preconfigured run. I also needed to run automake with an '--add-missing' tag, but I've been trying multiple work arounds and this may not be necessary, automake prompted me to add it though.

I just wanted to get a notice of this somewhere in case someone else runs into the problem

Been trying to compile the exonerate file but keep getting the bottom errors

DEPDIR=.deps depmode=none /bin/sh ../../depcomp
gcc -DPACKAGE_NAME="exonerate" -DPACKAGE_TARNAME="exonerate" -DPACKAGE_VERSION="2.4.0" -DPACKAGE_STRING="exonerate\ 2.4.0" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -DPACKAGE="exonerate" -DVERSION="2.4.0" -D_XOPEN_SOURCE=600 -DHAVE_DECL__XOPEN_PATH_MAX=0 -D_XOPEN_PATH_MAX=1024 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT=""lu"" -g -O2 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -c fsm.test.c
/bin/sh: ../../depcomp: No such file or directory
Makefile:396: recipe for target 'fsm.test.o' failed
make[2]: *** [fsm.test.o] Error 127
make[2]: Leaving directory '/home/bryan/exonerate/src/struct'
Makefile:258: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/bryan/exonerate/src'
Makefile:284: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1

Thanks

Bryan

Hi,
i been trying to run exonerate for est2genome module and here is the basic code (sorry im a newbie so dont know much about command line):
#!/bin/bash

#$ -S /bin/bash
#$ -cwd #Job runs in current directory -where submitted from
#$ -V #Job inherits current environment
#$ -pe smp.pe 8

#exonerate first trial for chunking the query database

exonerate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 1 --querychunktotal 8
exonerate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 2 --querychunktotal 8
exonerate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 3 --querychunktotal 8
exonerate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 4 --querychunktotal 8
exoberate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 5 --querychunktotal 8
exonerate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 6 --querychunktotal 8
exonerate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 7 --querychunktotal 8
exonerate /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/exonerate-2.2.0-x86_64 --model est2genome /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exo
nerate-2.2.0-x86_64/bin/transcripts.fasta /mnt/fls01-home01/mqbpkna2/scratch/January_2018/exonerate-2.2.0-x86_64/bin/Acomosus_321_v3.fa --querychunkid 8 --querychunktotal 8

exit 0

BUT. there is error: exo_1st_pineapple.sh: line 11: exonerate: command not found

please help me to solve this. thanks!

Hello, I get an error when I run 'make' during the process of installation.

My linux system:
Kernel Version: 5.15.0-58-generic
Operating System: Ubuntu 22.04.1 LTS
OSType: linux
Architecture: x86_64
CPUs: 8

Operating process:
$ git clone https://github.com/nathanweeks/exonerate.git
$ cd exonerate
$ ./configure
$ make
cd . && /home/howard/software/exonerate/missing aclocal-1.4
WARNING: aclocal-1.4' is needed, and you do not seem to have it handy on your system. You might have modified some files without having the proper tools for further handling them. Check the README' file,
it often tells you about the needed prerequirements for installing
this package. You may also peek at any GNU archive site, in case
some other package would contain this missing `aclocal-1.4' program.
make: *** [Makefile:108：aclocal.m4] error 1

Thank you!

dcb@dcb-OptiPlex-3020:~/Documents/sof/exonerate-master$ sudo make
Making all in doc
make[1]: Entering directory /home/dcb/Documents/sof/exonerate-master/doc' Making all in man make[2]: Entering directory /home/dcb/Documents/sof/exonerate-master/doc/man'
Making all in man1
make[3]: Entering directory /home/dcb/Documents/sof/exonerate-master/doc/man/man1' make[3]: Nothing to be done for all'.
make[3]: Leaving directory /home/dcb/Documents/sof/exonerate-master/doc/man/man1' make[3]: Entering directory /home/dcb/Documents/sof/exonerate-master/doc/man'
make[3]: Nothing to be done for all-am'. make[3]: Leaving directory /home/dcb/Documents/sof/exonerate-master/doc/man'
make[2]: Leaving directory /home/dcb/Documents/sof/exonerate-master/doc/man' make[2]: Entering directory /home/dcb/Documents/sof/exonerate-master/doc'
make[2]: Nothing to be done for all-am'. make[2]: Leaving directory /home/dcb/Documents/sof/exonerate-master/doc'
make[1]: Leaving directory /home/dcb/Documents/sof/exonerate-master/doc' Making all in src make[1]: Entering directory /home/dcb/Documents/sof/exonerate-master/src'
Making all in struct
make[2]: Entering directory /home/dcb/Documents/sof/exonerate-master/src/struct' gcc -DPACKAGE_NAME=\"exonerate\" -DPACKAGE_TARNAME=\"exonerate\" -DPACKAGE_VERSION=\"2.4.0\" -DPACKAGE_STRING=\"exonerate\ 2.4.0\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -D_XOPEN_SOURCE=600 -DHAVE_DECL__XOPEN_PATH_MAX=0 -D_XOPEN_PATH_MAX=1024 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT="\"lu\"" -g -O2 -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -MT fsm.test.o -MD -MP -MF .deps/fsm.test.Tpo -c -o fsm.test.o fsm.test.c In file included from fsm.test.c:17:0: fsm.h:24:37: fatal error: glib.h: No such file or directory #include <glib.h> /* For CHAR_BIT */ ^ compilation terminated. make[2]: *** [fsm.test.o] Error 1 make[2]: Leaving directory /home/dcb/Documents/sof/exonerate-master/src/struct'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/dcb/Documents/sof/exonerate-master/src'
make: *** [all-recursive] Error 1

The manual says:
"protein2genome
This model allows alignment of a protein sequence to genomic DNA. This is similar to the protein2dna model, with the addition of modelling of introns and intron phases. This model is simliar to those used by genewise."

I could not identify any difference between the protein2genome and protein2dna models.

I was wondering what to use in the case of data that should contain mostly coding sequences, but could contain introns, UTRs and anything beyond the genes. E.g. for hybrid enrichment data for which the bait region lies within the genes, but sequences could span beyond the coding region.
Here, modeling the introns could help in principle.
As far as I understand the manual, the protein2genome should be favoured for the described scenario. How are introns "modeled" in the two protein2dna and protein2genome cases.

Anytime I call the protein2genome:bestfit command I the program stalls out waiting for some unknown resources to being, but never gets them, even after hours. Here is an example command
exonerate --model protein2genome:bestfit
--maxintron 100
--percent 25
--showalignment true
--showtargetgff true
--showvulgar false
--query "./gene_cluster.fasta"
--target "./contig_2716_pilon_consensus.fasta"

Hi,
I got this error during the compilation:

$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking whether make sets $(MAKE)... yes
checking for working aclocal-1.4... missing
checking for working autoconf... missing
checking for working automake-1.4... missing
checking for working autoheader... missing
checking for working makeinfo... found
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for strings.h... (cached) yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking build system type... i386-apple-darwin17.2.0
checking host system type... i386-apple-darwin17.2.0
Set host to i386-apple-darwin17.2.0
i386-apple-darwin17.2.0
Customising build for OSX
Set source_root_dir to /Users/spribill/Downloads/exonerate-2.2.0/exonerate

checking for socklen_t... yes
checking for pkg-config... no
ERROR: Could not find pkg-config ... is glib-2 installed ???

The thing is that I have installed glib2-dev, according to the instruction in readme. I also installed glib2-shlibs, glibmm2.4-dev, and glibmm2.4-shlibs, since I've read that it might help, but it didn't.
For that I used the latest version of fink, if that matters.
Is there anything that could help?

Thank you,
Gulnara

I have gene models for a MaSuRCA assembly, but it's not a great assembly. I used the online tool CoGe to create a "pseudo assembly, where it maps the MaSuRCA contigs onto a higher quality reference for a more contiguous assembly. I want to transfer the gene models that were created for a MaSuRCA assembly to the "pseudo assembly" created by CoGe. The ultimate goal to to have a new .gff file.

I was able to install exonerate without errors on my university's Cluster. I first ran it on our debug partition that doesn't use much memory and it failed because it exceeded the memory I set (48 GB). Here is the command:

pseudo_assembly="/path/to/pseudo/assembly/pseudoassembly.faa"
gene_model="/path/to/gene/models/SFGP_GEN1Assembly.all.faa"
exonerate --model protein2genome -c 16 --showquerygff yes -q $gene_model -t $pseudo_assembly

Then I tried to run it on a larger partition that can handle up to 750 GB of Memory, but it experienced a segmentation fault. Here is the command:

exonerate --model protein2genome -c 32 --showquerygff yes -q $gene_model -t $pseudo_assembly

I saw that the only two parameters that dealt with memory were "--dpmemory" and "--fsmmemory", so I decided to max them out to the full memory I was allocating. The program ran, but failed after 30 minutes. Here is the command:

exonerate --model protein2genome -c 16 --showquerygff yes -M 500000 -D 500000 -q $gene_model -t $pseudo_assembly

The error was:
(process:52261): GLib-ERROR **: 11:17:13.991: gmem.c:105: failed to allocate 18446744072033491433 bytes

That is more bytes than I'll ever have access to. I tried lowering the -M and -D flags, but ended up with the same kind of error. Do you have any recommendations for fixing this error. Thanks!

configuration went smooth im stuck on the make step it shows an Error

Mu-Altamimis-Mac-Pro:exonerate-2.2.0 mohanad$ make
Making all in doc
Making all in man
Making all in man1
make[3]: Nothing to be done for `all'.
make[3]: Nothing to be done for `all-am'.
make[2]: Nothing to be done for `all-am'.
Making all in src
Making all in struct
gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.2.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I.      -g -O2 -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c
In file included from fsm.test.c:17:
./fsm.h:24:10: fatal error: 'glib.h' file not found
#include <glib.h> /* For CHAR_BIT */
         ^~~~~~~~
1 error generated.
make[2]: *** [fsm.test.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

please advise im kind of stuck

Hello, nathanweeks,
I recently had used EXONERATE in protein2genome alignments, but several species of error informations showed in this process as this title said. I checked your source code(opair.c), but I failed to understand why this lower score results this error-info. Also, if this meant results of those alignment are not optimal?

Best

Vincent

Hi,
is there a way to set exonerate to align each input query sequences in ungapped model (which is also the default model), without considering the sequence similarity or sequence length (also for sequences <20 bp for example) I'm trying to do a pairwise alignment of different clipped sequences with some reference Transposable Element sequences to see how good the clipped bases from short PE reads are aligning with reference TEs. It appears that exonerate has a certain threshold for similarity between sequences in order to report the alignment results, is it the case?

Note: "--percent 0" doesn't change anything on the result.

thanks,
Kiran

I must be doing something wrong here... but somehow it's looking for a "depcomp" tool that doesn't exist.

kelvin:exonerate (master) $ CC=gcc-4.8 ./configure
checking for a BSD-compatible install... /usr/local/bin/ginstall -c
checking whether build environment is sane... yes
/Users/dalexander/Downloads/exonerate/missing: Unknown --run' option Try/Users/dalexander/Downloads/exonerate/missing --help' for more information
configure: WARNING: 'missing' script is too old or missing
checking for a thread-safe mkdir -p... /usr/local/bin/gmkdir -p
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc-4.8
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.8 accepts -g... yes
checking for gcc-4.8 option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc-4.8... none
checking whether make sets $(MAKE)... (cached) yes
checking whether _XOPEN_PATH_MAX is declared... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking how to run the C preprocessor... gcc-4.8 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for strings.h... (cached) yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking build system type... i386-apple-darwin13.3.0
checking host system type... i386-apple-darwin13.3.0
Set host to i386-apple-darwin13.3.0
i386-apple-darwin13.3.0
Customising build for OSX

Set source_root_dir to /Users/dalexander/Downloads/exonerate

checking for socklen_t... yes
checking for pkg-config... /usr/local/bin/pkg-config
Using GLIB-2
Turning assertions off
Turning paranoid options off
Not using options for profiling with gprof
Not using options for analysis with gcov
Adding support for LARGE FILES (>2Gb) for a 32 bit system
Using COMPILED C4 MODELS

Installing UTILITIES

checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/man/Makefile
config.status: creating doc/man/man1/Makefile
config.status: creating src/Makefile
config.status: creating src/general/Makefile
config.status: creating src/sequence/Makefile
config.status: creating src/database/Makefile
config.status: creating src/struct/Makefile
config.status: creating src/comparison/Makefile
config.status: creating src/c4/Makefile
config.status: creating src/bsdp/Makefile
config.status: creating src/sdp/Makefile
config.status: creating src/hub/Makefile
config.status: creating src/model/Makefile
config.status: creating src/program/Makefile
config.status: creating src/util/Makefile
config.status: creating test/Makefile
config.status: creating test/util/Makefile
config.status: creating test/ipcress/Makefile
config.status: creating test/exonerate/Makefile
config.status: creating test/data/Makefile
config.status: creating test/data/cdna/Makefile
config.status: creating test/data/protein/Makefile
config.status: executing depfiles commands
kelvin:exonerate (master) $ make
Making all in doc
Making all in man
Making all in man1
make[3]: Nothing to be done for all'. make[3]: Nothing to be done forall-am'.
make[2]: Nothing to be done for `all-am'.
Making all in src
Making all in struct
source='fsm.test.c' object='fsm.test.o' libtool=no
DEPDIR=.deps depmode=none /bin/sh ../../depcomp
gcc-4.8 -DPACKAGE_NAME="exonerate" -DPACKAGE_TARNAME="exonerate" -DPACKAGE_VERSION="2.4.0" -DPACKAGE_STRING="exonerate\ 2.4.0" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -DPACKAGE="exonerate" -DVERSION="2.4.0" -D_XOPEN_SOURCE=600 -DHAVE_DECL__XOPEN_PATH_MAX=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -DCUSTOM_GUINT64_FORMAT=""llu"" -g -O2 -I/usr/local/Cellar/glib/2.40.0_1/include/glib-2.0 -I/usr/local/Cellar/glib/2.40.0_1/lib/glib-2.0/include -I/usr/local/opt/gettext/include -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -c fsm.test.c
/bin/sh: ../../depcomp: No such file or directory
make[2]: *** [fsm.test.o] Error 127
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
kelvin:exonerate (master) $

Hi all,

exonerate-2.4.0 compile fails on fedora 23 with this error:

gcc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.4.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I.  -DSOURCE_ROOT_DIR="\"/home/sagitter/rpmbuild/BUILD/exonerate-2.4.0\""            -DCUSTOM_GUINT64_FORMAT="\"lu\""            -I../../src/struct    -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -Wl,-z,relro -fPIC -pie -Wl,-z,now -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include  -c jobqueue.c
jobqueue.c: In function 'JobQueue_Task_free_func':
jobqueue.c:83:5: warning: implicit declaration of function 'JobQueue_Task_destroy' [-Wimplicit-function-declaration]
     JobQueue_Task_destroy(task);
     ^
jobqueue.c: In function 'JobQueue_submit':
jobqueue.c:109:7: error: 'JobQueue {aka struct <anonymous>}' has no member named 'job_func'
     jq->job_func(job_data); /* when no threads available, just run the job */
       ^
jobqueue.c: At top level:
jobqueue.c:81:13: warning: 'JobQueue_Task_free_func' defined but not used [-Wunused-function]
 static void JobQueue_Task_free_func(gpointer data, gpointer user_data){
             ^
Makefile:174: recipe for target 'jobqueue.o' failed

Full build log: http://fpaste.org/344263/
GCC-5.3.1

When I attempt to align SELENON RefSeq transcript NM_020451.2 with it's corresponding protein sequence (NP_065184.2), exonerate reports:

** FATAL ERROR **: Unknown amino acid [U]
exiting ...

This suggests that selenocysteine is not being handled correctly in spite of me using the most recent patched version:

exonerate from exonerate version 2.4.0
Using glib version 2.56.1
Built on Apr 25 2023

Any guidance on this would be appreciated.