[mira_talk] Re: Mira addRead_Error Found diginorm multiplier of 0?
- From: fun ngs <ngsfun@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 31 Oct 2014 11:55:43 +0530
Thanks John,
I was bit worried if my mail was delivered or not. I would wait for Bastien
to reply back and suggest a solution.
On Thu, Oct 30, 2014 at 9:28 PM, John Nash <john.he.nash@xxxxxxxxx> wrote:
> I'm sure Bastien is worrying about it right now as we read this. He has a
> day job so we'll wait for him to get home, have dinner, and then fix it. He
> will probably ask you for some data files to be put in a dropbox.
>
> John
>
>
>
> On Oct 30, 2014, at 11:53 AM, fun ngs <ngsfun@xxxxxxxxx> wrote:
>
> Hello,
>
> Please can you suggest any solution for this issue.
>
> regards,
> pravin
>
>
>
> On Wed, Oct 29, 2014 at 7:38 PM, fun ngs <ngsfun@xxxxxxxxx> wrote:
>
>> Hello,
>>
>> I have utilize mira v4.9.1 for performing the assembly but it again
>> struck with an error.
>>
>> Following is the error.
>>
>> Information on current assembly object:
>>
>> AS_readpool: 54182226 reads.
>> AS_contigs: 0 contigs.
>> AS_bbcontigs: 0 contigs.
>> Mem used for reads: 192 (192 B)
>>
>> Memory used in assembly structures:
>> Eff. Size Free cap.
>> LostByAlign
>> AS_writtenskimhitsperid: 0 24 B 0 B
>> 0 B
>> AS_skim_edges: 0 24 B 0 B
>> 0 B
>> AS_adsfacts: 0 24 B 0 B
>> 0 B
>> AS_confirmed_edges: 0 24 B 0 B
>> 0 B
>> AS_permanent_overlap_bans: 1 24 B 0 B
>> 0 B
>> AS_readhitmiss: 0 24 B 0 B
>> 0 B
>> AS_readhmcovered: 0 24 B 0 B
>> 0 B
>> AS_count_rhm: 0 24 B 0 B
>> 0 B
>> AS_clipleft: 54182226 207 MiB 0 B
>> 0 B
>> AS_clipright: 54182226 207 MiB 0 B
>> 0 B
>> AS_used_ids: 54182226 52 MiB 0 B
>> 6 B
>> AS_multicopies: 0 52 MiB 52 MiB
>> 6 B
>> AS_hasmcoverlaps: 0 52 MiB 52 MiB
>> 6 B
>> AS_maxcoveragereached: 54182226 207 MiB 0 B
>> 0 B
>> AS_coverageperseqtype: 0 24 B 0 B
>> 0 B
>> AS_istroublemaker: 54182226 52 MiB 0 B
>> 6 B
>> AS_isdebris: 54182226 52 MiB 0 B
>> 6 B
>> AS_needalloverlaps: 54182226 52 MiB 0 B
>> 6 B
>> AS_readsforrepeatresolve: 0 40 B 0 B
>> 0 B
>> AS_allrmbsok: 0 207 MiB 207 MiB
>> 0 B
>> AS_probablermbsnotok: 0 207 MiB 207 MiB
>> 0 B
>> AS_weakrmbsnotok: 0 207 MiB 207 MiB
>> 0 B
>> AS_readmaytakeskim: 0 40 B 0 B
>> 0 B
>> AS_skimstaken: 0 40 B 0 B
>> 0 B
>> AS_numskimoverlaps: 0 24 B 0 B
>> 0 B
>> AS_numleftextendskims: 0 24 B 0 B
>> 0 B
>> AS_rightextendskims: 0 24 B 0 B
>> 0 B
>> AS_skimleftextendratio: 0 24 B 0 B
>> 0 B
>> AS_skimrightextendratio: 0 24 B 0 B
>> 0 B
>> AS_skimmegahubs: 0 24 B 0 B
>> 0 B
>> AS_usedtmpfiles: 38 1 KiB 0 B
>> 0 B
>> Total: 1625469008 (1.5 GiB)
>>
>>
>> ================================================================================
>> Dynamic s allocs: 0
>> Dynamic m allocs: 0
>> Align allocs: 0
>>
>> Internal logic/programming/debugging error (*sigh* this should not have
>> happened)
>>
>>
>> ********************************************************************************
>> * no shortcuts made, not ready for searching?
>> *
>>
>> ********************************************************************************
>> ->Thrown: bool HashStatistics<TVHASH_T>::priv_dn_TestSingleSeq(Read &
>> actread, vector<uint8> & dn_allow, vector<size_t> & dn_vhashindexes)
>> ->Caught: main
>>
>> Aborting process, probably due to an internal error.
>>
>> If you want to report the error, please do so on
>> http://sourceforge.net/p/mira-assembler/tickets/
>> and also give a short notice on the mira talk mailing list.
>>
>> If reporting, please do not delete the log and checkpoint directories,
>> there may
>> be files in them which could be needed to find the problem.
>> Subscribing / unsubscribing to mira talk, see:
>> //www.freelists.org/list/mira_talk
>>
>> CWD: /data/results/Ion_Services/2014/1H_2014/dr_mohan/host_denovo/denovo
>> Thank you for noticing that this is *NOT* a crash, but a
>> controlled program stop.
>> Failure, wrapped MIRA process aborted.
>>
>> I am also attaching within the assembly log files.
>>
>> regards,
>>
>> On Wed, Oct 29, 2014 at 12:18 PM, fun ngs <ngsfun@xxxxxxxxx> wrote:
>>
>>> Hello,
>>>
>>> Thanks for your reply. Let me first try the assembly with 4.9.1 version
>>> and come back with its outputs. I would update on this analysis.
>>>
>>> warm regards,
>>> Pravin
>>>
>>>
>>> On Tue, Oct 28, 2014 at 8:34 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>
>>> wrote:
>>>
>>>> > On October 28, 2014 at 1:08 PM fun ngs <ngsfun@xxxxxxxxx> wrote:
>>>> > I am using mira 4.0.2 for performing de novo transcriptome assembly
>>>> with
>>>> >around
>>>> > 55 million reads. Assembly ended up with an Internal error and
>>>> displayed the
>>>> > following logs.
>>>> >
>>>>
>>>> >********************************************************************************
>>>> > * E6AMB:05734:07288: Found diginorm multiplier of 0?
>>>>
>>>> > *
>>>> >
>>>>
>>>> >********************************************************************************
>>>>
>>>> I think that this is something I have fixed in the current development
>>>> version.
>>>> Can you please download 4.9.1 and give that one a try?
>>>>
>>>> Best,
>>>> Bastien
>>>>
>>>> PS: unfortunately, you will not be able to resume an assembly started
>>>> by 4.0.x
>>>> with a 4.9.x version. You will need to start it normally, I'm sorry for
>>>> the
>>>> inconvenience.
>>>>
>>>> --
>>>> You have received this mail because you are subscribed to the mira_talk
>>>> mailing list. For information on how to subscribe or unsubscribe, please
>>>> visit http://www.chevreux.org/mira_mailinglists.html
>>>>
>>>
>>>
>>
>
>
Other related posts:
