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

[Felix Bemm]

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/	START
>> 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