[mira_talk] Re: Several illumina insert sizes

Dear Bastien,

Thursday, July 14, 2011, 10:22:09 PM, you wrote:

> On Jul 14, 2011, at 14:36 , Nestor Zaburannyi wrote:
>> That would be excellent. However, please make sure that we can specify 
>> *several* libraries. Two or three is not enough even today.

> Current limit in MIRA is 65535 libraries ... that should be enough for quite 
> a while. And if not ... changing that to 2^32-1 is a matter of minutes.

>> Thanks, i will correct it. As i understand, the value of "<trace_name>" tag 
>> should be equivalent to the identifier line, except for anything counting 
>> from the first whitespace in that line?
>> Like X|YZ:123 in
>>> X|YZ:123 SOME+OTHER_INFO.F

> Correct. Both FASTA and FASTQ define the name as everything fro the second 
> character up to the first blank

>> I will report if the aforementioned change will help.

> Please do.

With the new *.xml file like this:

<?xml version="1.0"?>
<TRACE_VOLUME>
     <TRACE>
             <TRACE_NAME>PE|300|1:4:1:1426:1923#ATGTAA/1</TRACE_NAME>
             <TEMPLATE_ID>1:4:1:1426:1923#ATGTAA</TEMPLATE_ID>
             <INSERT_SIZE>300</INSERT_SIZE>
             <INSERT_STDEV>30</INSERT_STDEV>
             <TRACE_END>FORWARD</TRACE_END>
     </TRACE>
...

MIRA V3.4rc2 is using 128GB of RAM and has gone into swap...
It is stuck on 
"Merging data from XML trace info file /data/work/illumina.xml"
The file is 1.4GB.

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
62432 neza001   20   0  131g 114g 1748 R 100.0 91.1   8:49.49 mira
  499 root      20   0     0    0    0 R 75.0  0.0   0:35.31 kswapd1
  500 root      20   0     0    0    0 S 16.7  0.0   0:48.41 kswapd2

There are no duplicate records in the xml, i checked. Any ideas?

Sincerely yours
Nestor


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