[mira_talk] Re: Solexa Mapping Runtime
- From: Christian Schleberger <Christian.Schleberger@xxxxxxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 05 Aug 2010 14:58:08 +0200
Dear Bastien and Federico,
Thank you for your advice. I started a new run with rc3 and it's already
through all the steps after 30 min.
best regards
Christian
Bastien Chevreux wrote:
>> I have started a mapping job with mira a couple of days ago and until
>> now it is not finished. I am wondering how long it will take.
>>
>
> I guess you are using 3.2.0rc2. This version had a regression error leading
> to what you are seeing: incredibly long running times in mapping mode for
> Solexa.
>
>
>> From the manual I understood that a job like this would be finished in
>> max two days.
>>
>
> Version 3.2.0rc3 fixes this, the whole assembly shouldn't take longer than
> half an hour to an hour for your job.
>
> I am sorry for any inconvenience this problem may have caused you.
>
> Bastien
>
> ----- original message --------
>
> Subject: [mira_talk] Solexa Mapping Runtime
> Sent: Thu, 05 Aug 2010
> From: Christian Schleberger<Christian.Schleberger@xxxxxxxxxxxxxxxxxxxxxxxxx>
>
>
>> Dear all,
>>
>> I have started a mapping job with mira a couple of days ago and until
>> now it is not finished. I am wondering how long it will take. From the
>> manual I understood that a job like this would be finished in max two days.
>>
>>
>> Here are the details:
>>
>> The computer is a Intel Xeon 2.13 GHz with 8 cores and 12 GB RAM. The
>> mira version is 3.2.0rc2 64 bit.
>>
>> the job was started with:
>> ./mira --project=K12mut --fastq --job=mapping,genome,accurate,solexa
>> -AS:nop=1 -SB:lsd=yes:bsn=K12_wt:bft=gbf:bbq=30 >&log_assembly.txt &
>>
>>
>> #####part of the log file for the detailed data of the reads and the
>> backbone:
>>
>> Loading backbone from GBF file: K12mut_backbone_in.gbf
>> Done.
>> Adding sequences as backbones ... done.
>> Postprocessing backbone (this may take a while)
>> 1 to process
>> U00096_bb 4639675
>> Localtime: Fri Jul 30 14:14:51 2010
>>
>> Seeing strain 1: "K12_wt"
>> Generated 1 unique strain ids for 1 reads.
>> Strain "default" has 0 reads.
>> Strain "K12_wt" has 1 reads.
>> Loading data (Solexa) from FASTQ files,
>> Counting sequences in FASTQ file: found 6826967 sequences.
>> Solexa will load 6826967 reads.
>> Longest Sanger: 0
>> Longest 454: 0
>> Longest PacBio: 0
>> Longest Solexa: 38
>> Longest Solid: 0
>> Longest overall: 38
>> Total reads to load: 6826967
>>
>> #### the last statistics:
>> Contig id: 1
>> Contig length: 4640360
>>
>> Sanger 454 PacBio Solexa
>> Solid
>> Num. reads 1 0 0 82089
>> 0
>> 100% merged reads - - - 5399486
>> 0
>> Avg. read len 4639675 0 0 36
>> 0
>> Max. coverage 1 0 0 122
>> 0
>> Avg. coverage 1.000 0.000 0.000 43.031
>> 0.000
>>
>> Max. contig coverage: 123
>> Avg. contig coverage: 44.031
>>
>> Consensus contains: A: 1142233 C: 1179561 G: 1176933
>> T: 1140987 N: 0
>> IUPAC: 0 Funny: 0 *: 646
>> GC content: 50.790%
>>
>> #### This is the last step:
>> Gogo: mapping all 4 errors
>> Localtime: Wed Aug 4 13:03:29 2010
>>
>> Gogo: mapping all 5 errors
>> Localtime: Thu Aug 5 06:39:02 2010
>>
>> So it needed ~17h for this step.
>>
>>
>> Is there something wrong with the data? How many steps should still come?
>>
>> best regards
>>
>>
>> Christian
>>
>>
>>
>
> --- original message end ----
>
>
>
--
Dr. Christian Schleberger
Inst. für Pharmazeutische Wissenschaften
Pharmazeutische Biologie und Biotechnologie
Albert-Ludwigs-Universität Freiburg
Stefan-Meier-Str. 19 (VF)
D-79104 Freiburg
Tel: +49 761 203 6240
Fax: +49 761 203 8383
email: Christian.Schleberger(at)pharmazie.uni-freiburg.de
Other related posts:
