Hey All, maybe someone with a deeper knowledge of perl could help me out here.
Maker 3.01.04 was unpacked and all dependencies and external programs installed using the Build command. Also all the Genemark perl dependencies were installed. Build status now says everything looks good.
And indeed I can run maker and get a reasonable annotation provided I don't run GeneMark. If I put the Genemark mod file into maker_opts, every single contig fails with the error "ERROR: GeneMark Failed".
running genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/plattsad/apps/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m /home/plattsad/a_thaliana.mod -g /home/plattsad/apps/maker/gmes_linux_64_4/gmhmme3 -p /home/plattsad/probuild -o /tmp/maker_kjOMDY/ptg000004l.abinit_nomask.0.a_thaliana%2Emod.genemark /tmp/maker_kjOMDY/ptg000004l.abinit_nomask.0
#-------------------------------#
/home/plattsad/apps/maker/gmes_linux_64_4/gmhmme3 -m /tmp/MjEUSA584J/J7UxPnQU40_mod -o /tmp/MjEUSA584J/gm_dna.fa_1.lst -b /dev/null /tmp/MjEUSA584J/gm_dna.fa_1Undefined subroutine &POSIX::_exit called at /home/plattsad/apps/maker/bin/../lib/Widget/genemark/gmhmm_wrap line 206.
ERROR: Genemark failed
--> rank=NA, hostname=ubuntu
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:ptg000004l
ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:ptg000004l
examining contents of the fasta file and run log
Now the only place I can see that error being generated is within the genemark wrapper script, so I can get the wrapper to print out the command line it is executing and then pause. I can then run that command in bash since the tmp files are all present:
/home/plattsad/apps/maker/bin$ for x in {1..12}
> do
> /home/plattsad/apps/maker/gmes_linux_64_4/gmhmme3 -m /tmp/pFgjj5Mue3/S0OXPptrjm_mod -o /tmp/pFgjj5Mue3/gm_dna.fa_"$x".lst -b /dev/null /tmp/pFgjj5Mue3/gm_dna.fa_"$x"
> echo $?
> done
0
0
0
0
0
0
0
0
0
0
0
0
So all, the split files get processed without errors in bash, but the system command in the perl wrapper must be failing, so as to trigger the die command.
Anyone got any ideas? I know this has been an issue on and off over the years, but Genemark seems to be properly configured.
Hey All, maybe someone with a deeper knowledge of perl could help me out here.
Maker 3.01.04 was unpacked and all dependencies and external programs installed using the Build command. Also all the Genemark perl dependencies were installed. Build status now says everything looks good.
And indeed I can run maker and get a reasonable annotation provided I don't run GeneMark. If I put the Genemark mod file into maker_opts, every single contig fails with the error "ERROR: GeneMark Failed".
Now the only place I can see that error being generated is within the genemark wrapper script, so I can get the wrapper to print out the command line it is executing and then pause. I can then run that command in bash since the tmp files are all present:
So all, the split files get processed without errors in bash, but the system command in the perl wrapper must be failing, so as to trigger the die command.
Anyone got any ideas? I know this has been an issue on and off over the years, but Genemark seems to be properly configured.