[mira_talk] Re: Several illumina insert sizes
- From: Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>
- To: Bastien Chevreux <mira_talk@xxxxxxxxxxxxx>
- Date: Sat, 16 Jul 2011 00:52:31 +0200
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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