[maker-devel] maker doesn't pick up where it stopped

[Yunfei Guo]

Hi Carson,

I used quitet mode, here's stderr (I only show one 'now starting the
contig' msg). When I check maker master log upon restart by 'grep -ic
finished master_log', all 'finished' tags were gone.

A data structure will be created for you at:
/home/yunfeiguo/projects/fish/scaffold/makerrun_2013_04_29/GapCloser-Nigro-Min1k.maker.output/GapCloser-Nigro-Min1k
_datastore

To access files for individual sequences use the datastore index:
/home/yunfeiguo/projects/fish/scaffold/makerrun_2013_04_29/GapCloser-Nigro-Min1k.maker.output/GapCloser-Nigro-Min1k
_master_datastore_index.log

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold105
Length: 8761
#---------------------------------------------------------------------

...
MAKER WARNING: The file
GapCloser-Nigro-Min1k.maker.output/GapCloser-Nigro-Min1k_datastore/C8/27/scaffold5690//theVoid.scaffold5690/scaffold5690.0.HumanUCSCProteins%2Efasta.blastx
did not finish on the last run and must be erased
...
ERROR: Could not open
'/home/yunfeiguo/projects/fish/scaffold/makerrun_2013_04_29/GapCloser-Nigro-Min1k.maker.output/GapCloser-Nigro-Min1k_datastore/A4/F7/scaffold6034//theVoid.scaffold6034/scaffold6034.0.Srub%2Elib.specific.out'
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:scaffold6034

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold6034
...


On Mon, May 6, 2013 at 5:32 AM, Carson Holt <carsonhh at gmail.com> wrote:

> You would have to send me the captured STDERR.  MAKER will print out a
> number of messages whenever it restarts a contig, and will explain why it
> deletes any files before restarting.
>
> Thanks,
> Carson
>
>
> From: Yunfei Guo <guoyunfei1989 at gmail.com>
> Date: Friday, 3 May, 2013 12:33 PM
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] maker doesn't pick up where it stopped
>
> Dear MAKER community,
>
> I got a problem that maker doesn't pick up where it stopped last time,
> rather, it will discard all previous results.
>
> command:
> echo 'mpiexec -n 12 maker -q' | qsub -V -cwd -l h_vmem=2g -pe mpich 12
> maker version:
> 2.26
> mpich version:
> 1.5rc3
> in maker_opts:
> clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0
> = no
> clean_up=0 #removes theVoid directory with individual analysis files, 1 =
> yes, 0 = no
>
> It never happened before. Any advice?
>
> Thank you!
>
> Yunfei
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>
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