[mira_talk] Solexa Assembly
- From: "aayushmaan@xxxxxxxxxxxxxx" <aayushmaan@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 7 Jan 2011 06:43:22 -0500
Hi Bastien,
We are currently running assembly of a 4 mb genome using solexa paired end
100bp lenght & 200bp insert size & file size is 7.2 GB in fastq format.
Below are the call parameters:
/bin/bin/mira --project=b90a --fastq --job=denovo,genome,accurate,solexa
-highlyrepetitive SOLEXA_SETTINGS -GE:tismin=100:tismax=300
The process is stuck at the below spet for a week now:
Searching for possible overlaps:
Localtime: Sat Jan 1 00:46:10 2011
Now running threaded and partitioned skimmer with 208 partitions in 2
threads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
[90%] ....|.... [100%]
We checked the log folder and found that the size of the 2 files named
b90a_int_posmatchc_preassembly & b90a_int_posmatchf_preassembly is
constantly increasing. Now both files are 146 GB in size and mira is also
using a swap of 36 gb.
Should we let this run or stop the assembly?
Regards,
Aayushmaan Bansal
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