[mira_talk] Re: Solexa Mapping Runtime
- From: "Bastien Chevreux" <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 5 Aug 2010 13:26:56 +0200 (MEST)
> 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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