[mira_talk] Re: Assembling 454 and Solexa mate-pair data - rethinking ...
- From: "Martin A. Hansen" <mail@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 3 Sep 2009 11:11:19 +0200
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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