[mira_talk] Re: Solexa Mapping Runtime

> 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 ----


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