[mira_talk] Re: Assembling 454 and Solexa mate-pair data - rethinking ...

  • From: Davide Sassera <davide.sassera@xxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Thu, 03 Sep 2009 11:25:15 +0200

Ok, so
you started Aug 31 at 8 AM
pass 1 was completed Sep 2 at 2 PM
so it took 54 hours, multiply 54 by the number of passes and you have your total time 

A couple more things:
In my (limited) experience the first pass seems shorter than the others, so it's better to wait until pass2 is completed to get a better estimate This timing works if you are not swapping. I had one assembly in which my RAM was not sufficient, and the timing was way off. BTW swapping is never a good idea. Finally: you can see you already have the caf files for pass 1 and 2. The one for pass 2 is still being written, but the one from pass 1 is an complete albeit preliminary, assembly you can use. 

D.


I am rerunning. This is the content of the log folder:

maasha@node1:~/DATA/Assembly/M1/M1_d_log$ ll
total 26361128
-rw-r--r-- 1 maasha maasha  188547168 Sep  2 14:27 hashstat.bin
-rw-r--r-- 1 maasha maasha          0 Aug 31 08:32 M1_error_reads_invalid
-rw-r--r-- 1 maasha maasha 15129381 Sep 2 13:34 M1_info_consensustaglist.1.txt -rw-r--r-- 1 maasha maasha 8987688 Sep 3 11:08 M1_info_consensustaglist.2.txt -rw-r--r-- 1 maasha maasha 80087308 Sep 2 13:34 M1_info_contigreadlist_pass.1.txt -rw-r--r-- 1 maasha maasha 62008149 Sep 3 11:08 M1_info_contigreadlist_pass.2.txt -rw-r--r-- 1 maasha maasha 2792769 Sep 2 13:34 M1_info_contigstats_pass.1.txt -rw-r--r-- 1 maasha maasha 579575 Sep 3 11:08 M1_info_contigstats_pass.2.txt -rw-r--r-- 1 maasha maasha 6345975 Sep 2 13:34 M1_info_debrislist_pass.1.txt 
-rw-r--r-- 1 maasha maasha   14914533 Sep  2 14:24 M1_info_reads_tooshort
-rw-r--r-- 1 maasha maasha 244938193 Sep 2 13:34 M1_info_readtaglist.1.txt -rw-r--r-- 1 maasha maasha 205417596 Sep 3 11:08 M1_info_readtaglist.2.txt 
-rw-r--r-- 1 maasha maasha  120017700 Aug 31 08:39 M1_int_clippings.0.txt
-rw-r--r-- 1 maasha maasha 8764972992 Sep 2 15:09 M1_int_normalisedskims_pass.2.bin -rw-r--r-- 1 maasha maasha 3060060346 Sep 2 14:56 M1_int_posmatchc_pass.2.lst -rw-r--r-- 1 maasha maasha 851047558 Sep 2 15:43 M1_int_posmatchc_pass.2.lst.reduced -rw-r--r-- 1 maasha maasha 3372920158 Sep 2 14:56 M1_int_posmatchf_pass.2.lst -rw-r--r-- 1 maasha maasha 935718347 Sep 2 15:42 M1_int_posmatchf_pass.2.lst.reduced -rw-r--r-- 1 maasha maasha 0 Sep 2 14:29 M1_int_posmatch_megahubs_pass.2.lst -rw-r--r-- 1 maasha maasha 0 Aug 31 09:11 M1_int_posmatch_multicopystat_preassembly.0.txt -rw-r--r-- 1 maasha maasha 3683640 Sep 2 14:29 M1_int_skimmarknastyrepeats_nastyseq_pass.2.lst 
-rw-r--r-- 1 maasha maasha 2252349153 Sep  2 13:34 M1_out_pass.1.caf
-rw-r--r-- 1 maasha maasha 1826039470 Sep  3 11:08 M1_out_pass.2.caf
-rw-r--r-- 1 maasha maasha   89317586 Aug 31 08:33 M1_readpoolinfo.lst
-rw-r--r-- 1 maasha maasha 2902396972 Sep 2 16:06 miralog.ads_pass.2.adsfacts -rw-r--r-- 1 maasha maasha 70726055 Sep 2 16:12 miralog.ads_pass.2.adsfacts.pclusters -rw-r--r-- 1 maasha maasha 757200052 Sep 2 16:06 miralog.ads_pass.2.complement -rw-r--r-- 1 maasha maasha 833488289 Sep 2 15:55 miralog.ads_pass.2.forward -rw-r--r-- 1 maasha maasha 2410754 Sep 2 16:06 miralog.ads_pass.2.reject 
-rw-r--r-- 1 maasha maasha          0 Sep  2 14:24 miralog.noqualities
-rw-r--r-- 1 maasha maasha          0 Sep  2 14:24 miralog.usedids
-rw-r--r-- 1 maasha maasha 185004534 Sep 2 14:24 repeat_resolve.1.adsfacts -rw-r--r-- 1 maasha maasha 52385944 Sep 2 14:24 repeat_resolve.1.complement -rw-r--r-- 1 maasha maasha 54537499 Sep 2 14:16 repeat_resolve.1.forward 
-rw-r--r-- 1 maasha maasha    3057012 Sep  2 14:24 repeat_resolve.1.reject



Martin
On Thu, Sep 3, 2009 at 10:22 AM, Davide Sassera <davide.sassera@xxxxxxxx <mailto:davide.sassera@xxxxxxxx>> wrote: 

    Hi Martin,

    maybe you do not have it because if I recall correctly you deleted
    the _log folder.

    It is possible to see what pass you are in (mira assembly process
    takes a variable number of passes, usually up to 7) by checkin the
    log folder, which is created in every assembly.

    You can also calculate approximately how long it will take if you
    consider how many passes have been done and how many are still to
    be done.

    Davide




    Hm, I have no such file - and no txt file contain such info?

    find . -name "*.txt" | xargs grep -i "Pass:" -> no results



    Martin

    On Wed, Sep 2, 2009 at 8:23 PM, Bastien Chevreux
    <bach@xxxxxxxxxxxx <mailto:bach@xxxxxxxxxxxx>> wrote:

        On Mittwoch 02 September 2009 Martin A. Hansen wrote:
        > Or perhaps 99.9% :o) !!! How can you tell how far the
        process is?

        grep "Pass:" log_assembly.txt

        gives you the pass it currently is in.

        Bastien

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-- Davide Sassera 
    Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria Facoltà di Veterinaria 
    Università degli Studi di Milano
    Via Celoria 10, 20133, Milano, ITALY
    Tel: +39 0250318094
    Fax: +39 0250318095





--
Davide Sassera
Sezione di Patologia Generale e Parassitologia
Dipartimento di Patologia Animale, Igiene e Sanità Pubblica Veterinaria Facoltà di Veterinaria 
Università degli Studi di Milano
Via Celoria 10, 20133, Milano, ITALY
Tel: +39 0250318094
Fax: +39 0250318095

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