[maker-devel] Contigs failing - could not make datastore directory

[Carson Holt]

You can also try the 2.29 beta if you want (on the website).  Also when
MAKER exits, it tries to delete anything left behind in temporary folders,
so is it possible that it is creating space on exit after filling up /tmp?

Given that the issue seems to go away when you switch to another
directory, it suggests that this might be the kind of thing that is
specific to something about the current state of your your system.

Thanks,
Carson


On 10/5/13 10:09 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:

>Hi Carson,
>
>there is definitely no quota neither a full local tmp device. I changed
>to another tmp device, which is unfortunately residing on nfs but now it
>seems to work. I am using the latest version of maker (2.28). The
>complete job is running on a single machine with 32 mpi threads.
>
>Bests
>Felix
>
>Am 04.10.2013 20:21, schrieb Carson Holt:
>> Hi Felix,
>>
>> There are other potential issues as well, for example a file quota limit
>> set by your administrator or full local /tmp which will be unique to
>>each
>> node and cannot be queried directly from the root node on a cluster.
>>On a
>> cluster one node may also not have the NFS location mounted.  Or it
>>could
>> be system related, for example on ibrix NFS mounted systems you can get
>>a
>> weird filesystem issue with ghost files and directories when using MAKER
>> that can neither be created nor deleted.  Try running the failed contigs
>> in a different directory (even if it's on the same disk).  Also what
>> version of MAKER are you using?
>>
>> --Carson
>>
>>
>>
>> On 10/4/13 3:10 AM, "Felix Bemm" <felix.bemm at uni-wuerzburg.de> wrote:
>>
>>> Hi,
>>>
>>> I have a problem with Contigs failing like this:
>>>
>>> examining contents of the fasta file and run log
>>> ERROR: could not make datastore directory
>>> --> rank=11, hostname=r5n04
>>> ERROR: Failed while examining contents of the fasta file and run log
>>> ERROR: Chunk failed at level:0, tier_type:0
>>> FAILED CONTIG:MA_gen_v8.05_c31675
>>>
>>> There is enough space available on both the storage device and the tmp
>>> device that is being used. The datastore log files looks like this:
>>>
>>> MA_gen_v8.05_c1149              FAILED
>>> MA_gen_v8.05_c1153              FAILED
>>> MA_gen_v8.05_c1154              FAILED
>>> MA_gen_v8.05_c1155              FAILED
>>> MA_gen_v8.05_c1156              FAILED
>>>
>>> Since there is no datastore for this contigs, I can not provide any
>>>more
>>> informationen. Approx. 1/3 of the contigs were annotated, after that
>>> maker started to fail. It kept running for a while and finishing some
>>>of
>>> the contigs in the second or third try like this:
>>>
>>> MA_gen_v8.05_c4443		FAILED
>>> MA_gen_v8.05_c4443		FAILED
>>> 
>>>MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/	STA
>>>RT
>>> ED
>>> MA_gen_v8.05_c4443	MA_gen_v8.05M_datastore/A7/9B/MA_gen_v8.05_c4443/
>>> FINISHED
>>>
>>> Any ideas what can cause this problems?
>>>
>>> Best regards
>>> Felix
>>>
>>> --
>>> Felix Bemm
>>> Department of Bioinformatics
>>> University of Würzburg, Germany
>>> Tel: +49 931 - 31 83696
>>> Fax: +49 931 - 31 84552
>>> felix.bemm at uni-wuerzburg.de
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
>-- 
>Felix Bemm
>Department of Bioinformatics
>University of Würzburg, Germany
>Tel: +49 931 - 31 83696
>Fax: +49 931 - 31 84552
>felix.bemm at uni-wuerzburg.de