[maker-devel] MAKER question

[Carson Holt]

>From the status messages, I can tell that there was apparently some sort of failure the first time you ran MAKER and the program did not clean up all lock files.  When you reran MAKER, after waiting to see if the encountered lock files were updated, the program decided that the other MAKER process must have failed so it cleaned up the locks for it.  The next error indicates that RepeatMasker did not finish the last time you ran MAKER so it must delete the old contig-dpp-500-500.0.out before continuing.  Then when the program finally goes to run the contig it sees that it has already tried and failed twice.  Your control files are set to retry only 1 time, so MAKER skips this contig and moves on to the next one, and since there is no next one, MAKER exits.

Rerun MAKER with the -f option to destroy all old data and reset the failure count for this contig to 0 or just set retry to a higher number.  Your original failure seems to be related to RepeatMasker, so make sure you have configured RepeatMasker correctly.

Thanks,
Carson


On 12/9/09 9:12 AM, "Quentin Santana" <Quentin.Santana at fabi.up.ac.za> wrote:

Hi all

I have installed MAKER on our system and have tried to run the test data in a new test directory. However when I run MAKER, it outputs this. There must be something I am missing or have not done correctly. Any help will be greatly appreciated. I have also attached the log files for the config files.




x3:test maker$ maker maker_exe.ctl maker_opts.ctl maker_bopts.ctl
WARNING: Lock found, maker may already be running.
Checking for other instance.

Everything seems ok!!

A data structure will be created for you at:
/Users/maker/MAKER/test/dpp_contig.maker.output/dpp_contig_datastore

To access files for individual sequences use the datastore index:
/Users/maker/MAKER/test/dpp_contig.maker.output/dpp_contig_master_datastore_index.log




--Next Contig--

Processing run.log file...
MAKER WARNING: The file dpp_contig.maker.output/dpp_contig_datastore/contig-dpp-500-500/theVoid.contig-dpp-500-500/contig-dpp-500-500.0.out
did not finish on the last run and must be erased
#---------------------------------------------------------------------
The contig failed 2 time!!
Maker will not try again!!
The contig will be stored in a fasta file that you can use for debugging.
SeqID: contig-dpp-500-500
Length: 32156
FASTA: /Users/maker/MAKER/test/dpp_contig.maker.output/dpp_contig_datastore/contig-dpp-500-500/contig-dpp-500-500.died.fasta
#---------------------------------------------------------------------




Maker is now finished!!!



Regards
Quentin


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