Hi. I'm Lee.
I'm now running Metassembler using Pig-tailed rhesus data(154G).
it works well(bowtie2, mateAn, etc) but have problem in MUMmer : [TIME].
I searched and changed MUMmer because my reference sequence is larger than is supported by default.
After changing, It makes another file (B.A.ntref - 3G , B.A.mgaps - 140G).
I think it is used when making B.A.delta. but it take too much time ( 17 days now and still working - 43G).
Is there any method to reduce time like parallel processing?
And I want to know how much time it take when using human sequence data.
Thanks you.
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You should try usign different -l and -c paramteres for nucmer (this can be
done with the parameters nucmer_l and nucmer_c in the conf file). For large
or very repetitive genomes I would recommend: -l 100 -c 500; and if it
still takes too much time use -l 250 anc -c 500. This two parameters can be
used to leverage sensitivity and computational load in the whole genome
alignment step, please refer to the nucmer manual for further explanation
of what they do exactly.
Hi. I'm Lee.
I'm now running Metassembler using Pig-tailed rhesus data(154G).
it works well(bowtie2, mateAn, etc) but have problem in MUMmer : [TIME].
I searched and changed MUMmer because my reference sequence is larger than
is supported by default.
After changing, It makes another file (B.A.ntref - 3G , B.A.mgaps - 140G).
I think it is used when making B.A.delta. but it take too much time ( 17
days now and still working - 43G).
Is there any method to reduce time like parallel processing?
And I want to know how much time it take when using human sequence data.
It will require a bit of code editing, but can get the job done
Good luck
Mike
On Wed, Aug 30, 2017 at 11:20 AM, Alejandro Hernandez Wences
ahwences@users.sf.net wrote:
You should try usign different -l and -c paramteres for nucmer (this can be
done with the parameters nucmer_l and nucmer_c in the conf file). For large
or very repetitive genomes I would recommend: -l 100 -c 500; and if it
still takes too much time use -l 250 anc -c 500. This two parameters can be
used to leverage sensitivity and computational load in the whole genome
alignment step, please refer to the nucmer manual for further explanation
of what they do exactly.
Hi. I'm Lee.
I'm now running Metassembler using Pig-tailed rhesus data(154G).
it works well(bowtie2, mateAn, etc) but have problem in MUMmer : [TIME].
I searched and changed MUMmer because my reference sequence is larger
than
is supported by default.
After changing, It makes another file (B.A.ntref - 3G , B.A.mgaps -
140G).
I think it is used when making B.A.delta. but it take too much time ( 17
days now and still working - 43G).
Is there any method to reduce time like parallel processing?
And I want to know how much time it take when using human sequence data.
Hi. I'm Lee.
I'm now running Metassembler using Pig-tailed rhesus data(154G).
it works well(bowtie2, mateAn, etc) but have problem in MUMmer : [TIME].
I searched and changed MUMmer because my reference sequence is larger than is supported by default.
After changing, It makes another file (B.A.ntref - 3G , B.A.mgaps - 140G).
I think it is used when making B.A.delta. but it take too much time ( 17 days now and still working - 43G).
Is there any method to reduce time like parallel processing?
And I want to know how much time it take when using human sequence data.
Thanks you.
You should try usign different -l and -c paramteres for nucmer (this can be
done with the parameters nucmer_l and nucmer_c in the conf file). For large
or very repetitive genomes I would recommend: -l 100 -c 500; and if it
still takes too much time use -l 250 anc -c 500. This two parameters can be
used to leverage sensitivity and computational load in the whole genome
alignment step, please refer to the nucmer manual for further explanation
of what they do exactly.
On Tue, Aug 29, 2017 at 11:59 PM, HoYong LEE hystar@users.sf.net wrote:
There is also a script here that can be used to run the alignments in
parallel on an sge-based grid:
https://github.com/fritzsedlazeck/sge_mummer
It will require a bit of code editing, but can get the job done
Good luck
Mike
On Wed, Aug 30, 2017 at 11:20 AM, Alejandro Hernandez Wences ahwences@users.sf.net wrote: