[mira_talk] Re: Skim hits error
- From: "Shabhonam Caim (TGAC)" <Shabhonam.Caim@xxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 30 Sep 2010 10:20:06 +0100
Hi Bastien
Thanks for your reply, the whole log directory is around 680Gb, so I cannot
send you the whole log, but if you can tell me which files are you interested
in, I can send you those. But I am still pasting some information:
total 680G
-rw-r--r-- 1 toselana ga002 0 Sep 17 17:17 draft_error_reads_invalid
-rw-r--r-- 1 toselana ga002 23M Sep 18 02:49 draft_info_reads_tooshort
-rw-r--r-- 1 toselana ga002 2.0G Sep 19 02:34 draft_int_clippings.0.txt
-rw-r--r-- 1 toselana ga002 430G Sep 19 18:52
draft_int_normalisedskims_preassembly.0.bin
-rw-r--r-- 1 toselana ga002 117G Sep 19 02:34
draft_int_posmatchc_preassembly.0.lst
-rw-r--r-- 1 toselana ga002 127G Sep 19 02:34
draft_int_posmatchf_preassembly.0.lst
-rw-r--r-- 1 toselana ga002 0 Sep 18 08:02
draft_int_posmatch_megahubs_preassembly.0.lst
-rw-r--r-- 1 toselana ga002 0 Sep 19 02:34
draft_int_posmatch_multicopystat_preassembly.0.txt
-rw-r--r-- 1 toselana ga002 1.1G Sep 17 17:22 draft_readpoolinfo.lst
-rw-r--r-- 1 toselana ga002 2.9G Sep 18 07:08 hashstat.bin
-rw-r--r-- 1 toselana ga002 0 Sep 18 02:50 miralog.noqualities
-rw-r--r-- 1 toselana ga002 780M Sep 18 02:50 miralog.usedids
Thanks for your help.
Cheers
Shab
-----Original Message-----
From: mira_talk-bounce@xxxxxxxxxxxxx [mailto:mira_talk-bounce@xxxxxxxxxxxxx] On
Behalf Of Bastien Chevreux
Sent: 28 September 2010 20:58
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Re: Skim hits error
On Donnerstag 23 September 2010 Shabhonam Caim (TGAC) wrote:
> Assembly with 1 Lane of Illumina ~32 million reads
> About 1.5 million 454 reads
Hello Shab,
I fear that this will be one of the projects where MIRA has to capitulate. You
are operating at the border of what MIRA can theoretically handle ... and
crossed it.
> Expected genome size ~150 Mb
> Having to write log files to NFS drive
That is ... bad.
> I did try the miramem and I got the memory estimate around 80Gb, but its
> utilising over 200Gb of memory.
Can you please send me the whole log file? I'd like to know where the memory
goes.
> Here is the latest error message from MIRA.
> [...]
> "More than 2^31 skim hits would be taken ... this was not foreseen yet.
> Please contact the author."
That's the boundary the project crosses. I'm working on something to alleviate
this problem, but it will take some time before I can roll that out, I first
have a bug fix version on my list.
Best,
Bastien
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