[maker-devel] ERROR: Could not obtain lock to format database

[Hung-Wei Hsu]

I make sure I just ran one instance of MAKER at the same time.
I only analyzed one contig for the test.
After MAKER interruption, I can't find an GFF3 output of this contig.
There are only a theVoidXXX directory and a run.log file.

I'm trying 2.26b with the same parameters for the same data.
Hopefully, it can work well.

Hung-Wei


2013/3/16 Carson Holt <carsonhh at gmail.com>

> Were you by any chance running multiple instances of MAKER at the same
> time in the same directory?  It looks like two processes started to work on
> the same contig (normally a first set of locks blocks this possibility –
> but rarely they get past that step).  Then when it got to a part where an
> analysis is performed one properly failed when it realized that the other
> had the lock.  In any case, it looks like it just retried and finished the
> contig in question.  So the snippet seems to indicate expected behavior.
>  Do you see the contig in question as being finished and having an output
> GFF3?
>
> --Carson
>
>
>
>
> From: Hung-Wei Hsu <ares711122 at gmail.com>
> Date: Thursday, 14 March, 2013 11:13 PM
> To: Carson Holt <carsonhh at gmail.com>
> Cc: <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] ERROR: Could not obtain lock to format database
>
> You may find the error messages in the run log as attached.
> Thanks a lot in advance.
>
> Best regards,
> Hung-Wei
>
>
> 2013/3/14 Carson Holt <carsonhh at gmail.com>
>
>> Could you check to make sure your hard drive is not full, whatever
>> location you set as TMP= in the control files is not full (default is
>> /tmp).  Also maker sure you do not set /tmp to an NFS mounted or a tmpfs
>> location.
>>
>> Could you also send the full captured STDERR.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: Hung-Wei Hsu <ares711122 at gmail.com>
>> Date: Tuesday, 12 March, 2013 8:24 PM
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] ERROR: Could not obtain lock to format database
>>
>> Hi MAKER developers,
>>
>> I tried MAKER 2.27b on one E. coli scaffold sequence with uniprot protein
>> database.
>> I failed to run the analysis and got an error message as below.
>>
>> Could not obtain lock to format database at maker-2.27b/bin/../lib/GI.pm
>>
>> Any suggestions or helps will be deeply appreciated.
>>
>> Best regards,
>> Hung-Wei
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
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