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

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>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>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
>
>

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