[mira_talk] Re: Regarding combination of paired-end library and unpaired data set in mira
- From: Ganga Jeena <ganga.jeena@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 14 Dec 2010 09:31:41 +0530
The attached is log file of mira run for 7995476 reads in a 500 GB 48
processors system with 270 GB memory.
The program showed exit status with 240 GB of reads_d_log directory,
nothing within reads_d_results. I feel the assembly exited owing to lack of
storage space.
But for what reason, such a large number of similar reads, show up
*AS_contigs:
0 contigs *
Please explain.
Regards,
Ganga Jeena
Information on current assembly object:
AS_readpool: 7995476 reads.
*AS_contigs: 0 contigs.
AS_bbcontigs: 0 contigs.*
Mem used for reads: 31438549904 (29.3 GiB)
Memory used in assembly structures:
Eff. Size Free cap. LostByAlign
AS_writtenskimhitsperid: 7995476 31 MiB 0 B 0 B
AS_skim_edges: 9139243936 272.4 GiB 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: 0 366 MiB 0 B 0 B
AS_readhitmiss:
(END)
On Tue, Dec 14, 2010 at 9:07 AM, Ganga Jeena <ganga.jeena@xxxxxxxxx> wrote:
> Dear Sir,
>
> m using sff_extract version '0.2.8'
> Regards,
>
>
>
>
> On Tue, Dec 14, 2010 at 4:54 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> On Montag 13 Dezember 2010 Ganga Jeena wrote:
>> > 1)
>> > I want to assemble the combination of 3kb-Paired End, 8kb Paired End,
>> 35000
>> > reads (single-end) data.
>> > Should I combine uppaired and paired end data into one file as an input
>> to
>> > mira ?
>>
>> Yes, as shown in the docs.
>>
>> > 2)
>> > *sff_extract -o cp -a -l linker.fasta -i "insert_size:8000,
>> > insert_stdev:1000" /data/13_Dec/GSMQLLJ01.sff*
>> > *[Errno 22] Invalid argument*
>>
>> Ummm ... works for me? Which version of sff_extract?
>>
>> B.
>>
>> --
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>
>
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