Ran into unknown state (hex char: 29) at /home/a200302/maker-2.10/lib/File/..//Proc/Signal.pm line 94.

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Ran into unknown state (hex char: 29) at /home/a200302/maker-2.10/lib/File/..//Proc/Signal.pm line 94.

Phil
Hi,

due to the help of a colleague I was able to set up maker on our local
cluster, which is great as I can run >150 maker processes in the same
folder (not mpi, just a lot of parallel processes on differing nodes).
However, there is one error message popping up all the time. It does
not seem to affect output, as I ran maker on the same data on my iMac
for some time and the annotations seemed to be the same. Also we had a
look at the file and didn't think the message to be relevant. Still
I'd be interested to know what is wrong.
(Just one thing I am running WU-blast now on the server as the ncbi+
makeblastdb stopped working for some reason and I hadn't got the nerve
to fix it at that time. The error however also came up when ncbi was
still working). Please find an example output below.

Cheers,

Phil

/home/axyz/wu_blast/blasta
/home/axyz/wu_blast/BLOSUM62
Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.
WARNING: Multiple MAKER processes have been started in the
same directory.

Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.
Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.
A data structure will be created for you at:
/scratch/roman/maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_datastore
To access files for individual sequences use the datastore index:/
scratch/roman/maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_master_datastore_index.log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold72.1_size82174
Length: 82174
#---------------------------------------------------------------------


Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.running  repeat masker.#---------
command -------------#
Widget::RepeatMasker:
/home/axyz/RepeatMasker/RepeatMasker /scratch/roman/
maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_datastore/53/68/scaffo
ld72.1_size82174//theVoid.scaffold72.1_size82174/
scaffold72%2E1_size82174.0.all.rb -species all -dir /scratch/roman/
maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m3
0dev05lib2-20-sd-nr0_2.final.scaffolds_datastore/53/68/
scaffold72.1_size82174//theVoid.scaffold72.1_size82174 -pa 4
#-------------------------------#processing output: cycle 1
cycle 2 cycle 3 cycle 4
cycle 5
cycle 6
cycle 7
cycle 8
cycle 9 cycle 10 Generating output...
maskingdoneformating database...#--------- command -------------#
Widget::formater:/home/axyz/wu_blast/xdformat -p /scratch/romtmpKA/
maker_po35vG/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
XDFORMAT-WashU 1.0 [04-May-2006] [linux24-x64-I32LPF64
2006-05-11T11:16:32]
Start:  2011-06-06T21:54:31
XDF Output Database:  /scratch/romtmpKA/maker_po35vG/te_proteins
%2Efasta.mpi.10.0
 Alphabet:  NCBIstdaa(1)Input: "/scratch/romtmpKA/maker_po35vG/
te_proteins%2Efasta.mpi.10.0" No. of sequences (letters) written:
2492  (955,337)
 Longest sequence written (in database):  2485  (2485)
Total cpu time:  0.01u 0.02s 0.03t   Elapsed:  00:00:00
End:  2011-06-06T21:54:31Ran into unknown state (hex char: 29) at /
home/axyz/maker-2.10/lib/File/..//Proc/Signal.pm line 94.running
blast search.
#--------- command -------------#Widget::blastx:
/scratch/romtmpKA/maker_po35vG/blastx /scratch/romtmpKA/maker_po35vG/
te_proteins%2Efasta.mpi.10.0 /scratch/romtmpKA/maker_po35vG/rank0/
scaffold72%2E1_size82174.0 B=10000 V=10000 E=1e-06 wordmask=seg Z=300
Y=500000000 hspmax=100 cpus=4 gspmax=100 lcmask maskextra=10 kap gi
warnings notes novalidctxok nonnegok shortqueryok -o /scratch/roman/
maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_datastore/53/68/scaffold72.1_size82174//
theVoid.scaffold72.1_size82174/scaffold72%2E1_size82174.0.te_proteins
%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.
10.0.repeatrunner#-------------------------------#
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/home/axyz/wu_blast/xdformat -p /scratch/romtmpKA/maker_po35vG/
te_proteins%2Efasta.mpi.10.1

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Re: Ran into unknown state (hex char: 29) at /home/a200302/maker-2.10/lib/File/..//Proc/Signal.pm line 94.

Carson Hinton Holt
Re: [maker-devel] Ran into unknown state (hex char: 29) at /home/a200302/maker-2.10/lib/File/..//Proc/Signal.pm line 94. The error is being thrown by a module that is used to check on other running processes when multiple instances of MAKER are running.  You may be able to fix it by updating Proc::ProcessTable from CPAN, which is a dependency of Proc::Signal.  Could you let me know what your OS is, as this is likely going to be an OS specific issue.

The error won’t affect MAKER analysis.  The only potential side effect of the error is the existence of a handful of zombie processes that will not clean themselves up until after MAKER exits.  Proc::Signal is checking on certain support processes and cleaning them up properly when needed, so the error could cause them to only be cleaned up at the end of the program.  This will not affect analyses, it just produces annoying messages when you use “top” and “ps” in Linux.

Thanks,
Carson



On 6/6/11 2:13 PM, "Phil" <philipp.schiffer@...> wrote:

Hi,

due to the help of a colleague I was able to set up maker on our local
cluster, which is great as I can run >150 maker processes in the same
folder (not mpi, just a lot of parallel processes on differing nodes).
However, there is one error message popping up all the time. It does
not seem to affect output, as I ran maker on the same data on my iMac
for some time and the annotations seemed to be the same. Also we had a
look at the file and didn't think the message to be relevant. Still
I'd be interested to know what is wrong.
(Just one thing I am running WU-blast now on the server as the ncbi+
makeblastdb stopped working for some reason and I hadn't got the nerve
to fix it at that time. The error however also came up when ncbi was
still working). Please find an example output below.

Cheers,

Phil

/home/axyz/wu_blast/blasta
/home/axyz/wu_blast/BLOSUM62
Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.
WARNING: Multiple MAKER processes have been started in the
same directory.

Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.
Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.
A data structure will be created for you at:
/scratch/roman/maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_datastore
To access files for individual sequences use the datastore index:/
scratch/roman/maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_master_datastore_index.log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold72.1_size82174
Length: 82174
#---------------------------------------------------------------------


Ran into unknown state (hex char: 29) at /home/axyz/maker-2.10/lib/
File/..//Proc/Signal.pm line 94.running  repeat masker.#---------
command -------------#
Widget::RepeatMasker:
/home/axyz/RepeatMasker/RepeatMasker /scratch/roman/
maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_datastore/53/68/scaffo
ld72.1_size82174//theVoid.scaffold72.1_size82174/
scaffold72%2E1_size82174.0.all.rb -species all -dir /scratch/roman/
maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m3
0dev05lib2-20-sd-nr0_2.final.scaffolds_datastore/53/68/
scaffold72.1_size82174//theVoid.scaffold72.1_size82174 -pa 4
#-------------------------------#processing output: cycle 1
cycle 2 cycle 3 cycle 4
cycle 5
cycle 6
cycle 7
cycle 8
cycle 9 cycle 10 Generating output...
maskingdoneformating database...#--------- command -------------#
Widget::formater:/home/axyz/wu_blast/xdformat -p /scratch/romtmpKA/
maker_po35vG/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
XDFORMAT-WashU 1.0 [04-May-2006] [linux24-x64-I32LPF64
2006-05-11T11:16:32]
Start:  2011-06-06T21:54:31
XDF Output Database:  /scratch/romtmpKA/maker_po35vG/te_proteins
%2Efasta.mpi.10.0
 Alphabet:  NCBIstdaa(1)Input: "/scratch/romtmpKA/maker_po35vG/
te_proteins%2Efasta.mpi.10.0" No. of sequences (letters) written:
2492  (955,337)
 Longest sequence written (in database):  2485  (2485)
Total cpu time:  0.01u 0.02s 0.03t   Elapsed:  00:00:00
End:  2011-06-06T21:54:31Ran into unknown state (hex char: 29) at /
home/axyz/maker-2.10/lib/File/..//Proc/Signal.pm line 94.running
blast search.
#--------- command -------------#Widget::blastx:
/scratch/romtmpKA/maker_po35vG/blastx /scratch/romtmpKA/maker_po35vG/
te_proteins%2Efasta.mpi.10.0 /scratch/romtmpKA/maker_po35vG/rank0/
scaffold72%2E1_size82174.0 B=10000 V=10000 E=1e-06 wordmask=seg Z=300
Y=500000000 hspmax=100 cpus=4 gspmax=100 lcmask maskextra=10 kap gi
warnings notes novalidctxok nonnegok shortqueryok -o /scratch/roman/
maker_FREEZE1_rom2_snap/FREEZE_rom_clc2_allnewPE.fasta-
x1m30dev05lib2-20-sd-nr0_2.final.scaffolds.maker.output/
FREEZE_rom_clc2_allnewPE.fasta-x1m30dev05lib2-20-sd-
nr0_2.final.scaffolds_datastore/53/68/scaffold72.1_size82174//
theVoid.scaffold72.1_size82174/scaffold72%2E1_size82174.0.te_proteins
%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.
10.0.repeatrunner#-------------------------------#
deleted:0 hits
formating database...
#--------- command -------------#
Widget::formater:
/home/axyz/wu_blast/xdformat -p /scratch/romtmpKA/maker_po35vG/
te_proteins%2Efasta.mpi.10.1

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Carson Holt
Graduate Student
Yandell Lab
http:/www.yandell-lab.org/
Eccles Institute of Human Genetics
University of Utah

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