Closed peritob closed 6 years ago
If a block to block comparison has completed successfully, then yes, you do not have to repeat it. That is your answer to 2. is yes, you don't have to do DB.5 versus DB.4 again.
With -t100, I could see memory ocassionally spiking severely depending
on the sequence
content of the blocks being compared. This is probably why the jobs
terminate -- over physical
memory limit, go to virtual memory and then takes so long, it gets
knocked off the queue without
completing all jobs. But I'm guessing. Regardless it is better to use
the -M parameter to set the
maximum amount of memory available to daligner and not use the -t
parameter at all. By setting
say -M16, daligner will self adjust "-t" so that exactly 16Gbp is used.
In our experience with
blocks of 200-250Mbp, the value of -t used gives more than enough
sensitivity.
-- Gene
On 4/22/18, 8:54 AM, peritob wrote:
|daligner -v -b -k16 -t100 -Dlocalhost:1234 -r1 -j16 DB.5 DB.4 DB.3 DB.2 DB.1|
My apologies for not fully understanding your very detailed explanation and thanks in advance for your help.
I am using the HPC.daligner script within the Marvel assembler. One of the script lines is above. I frequently run out of resources and have to restart with perhaps only: DB.5.DB.5.las and DB.5.DB.4.las apparently completed based on the output.txt.
Two questions:
1.
Will daligner restart from the last point and continue on appropriately? (I keep checkpoint files for restarts)
2.
It appears that each step of alignment completes before moving to the next. Does this imply that the script can be altered to the files that have completed? For example, as the DB.5.DB.4.las completed can I change the script to:
|daligner -v -b -k16 -t100 -Dlocalhost:53778 -r1 -j16 DB.5 DB.3 DB.2 DB.1|
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Thanks for your help.
daligner -v -b -k16 -t100 -Dlocalhost:1234 -r1 -j16 DB.5 DB.4 DB.3 DB.2 DB.1
My apologies for not fully understanding your very detailed explanation and thanks in advance for your help.
I am using the HPC.daligner script within the Marvel assembler. One of the script lines is above. I frequently run out of resources and have to restart with perhaps only: DB.5.DB.5.las and DB.5.DB.4.las apparently completed based on the output.txt.
Two questions:
Will daligner restart from the last point and continue on appropriately? (I keep checkpoint files for restarts)
It appears that each step of alignment completes before moving to the next. Does this imply that the script can be altered to the files that have completed? For example, as the DB.5.DB.4.las completed can I change the script to:
daligner -v -b -k16 -t100 -Dlocalhost:53778 -r1 -j16 DB.5 DB.3 DB.2 DB.1