Hi,
Le 2012-05-18 13:31, nikos ioannidis a écrit :
> hello,
>
>
>
> i have set the minimum coverage at 40 with kmar size at 35 of a
> bacteria and i get this output:
>
This are usually well detected automatically.
>
>
>
> 861 Rank 0: the minimum coverage is 40
> 862 Rank 0: the peak coverage is 8
> 863 Rank 0: Assembler panic: no peak observed in the k-mer coverage
> distribution.
> 864 Rank 0: to deal with the sequencing error rate, try to lower the
> k-mer length (-k)
> 865 Rank 15: sent 50519 messages, received 50520 messages.
> 866 Rank 14: sent 50583 messages, received 50584 messages.
> 867 Rank 13: sent 50504 messages, received 50505 messages.
> 868 Rank 12: sent 50565 messages, received 50566 messages.
> 869 Rank 11: sent 50318 messages, received 50319 messages.
> 870 Rank 10: sent 50318 messages, received 50319 messages.
> 871 Rank 9: sent 50328 messages, received 50329 messages.
> 872 Rank 8: sent 50590 messages, received 50591 messages.
> 873 Rank 7: sent 50494 messages, received 50495 messages.
> 874 Rank 6: sent 50421 messages, received 50422 messages.
> 875 Rank 5: sent 50401 messages, received 50402 messages.
> 876 Rank 4: sent 72261 messages, received 72262 messages.
> 877 Rank 3: sent 118348 messages, received 118349 messages.
> 878 Rank 2: sent 118723 messages, received 118724 messages.
> 879 Rank 1: sent 118452 messages, received 118453 messages.
> 880 Rank 0: sent 118589 messages, received 118573 messages.
>
> how can i set the average coverage? Because all the papers i see have
> examined at coverage of N50, N40 , N30
>
>
You should not have to set these values in Ray in general.
N50 and friends are not related to the coverage depth.
>
>
> also by this output i want to ask you if i'm running in parallel, the
> Rank symbolize the spesific CPU/ task??
>
Yes, a rank identifies a process running on a processor core.
> i gave this commant:
>
>
> 14 srun ~/Ray-1.7/Ray -n 16 -k 35 -minimumCoverage 40 \
> 15 -p ~/Staphylococcus_aureus/frag_1.fastq
> ~/Staphylococcus_aureus/frag_2.fastq\
> 16 -p ~/Staphylococcus_aureus/shortjump_1.fastq
> ~/Staphylococcus_aureus/shortjump_2.fastq\
> 17 -o Staphy1635c40
I think this command won't work as expected. It will run Ray on 1
processor core.
The "-n 16" should be given to srun, not Ray.
To launch Ray on 16 processor cores, you must start Ray with mpiexec.
Just like this:
mpiexec -n 16 ~/Ray-1.7/Ray -k 31 \
-p ~/Staphylococcus_aureus/frag_1.fastq
~/Staphylococcus_aureus/frag_2.fastq \
-p ~/Staphylococcus_aureus/shortjump_1.fastq
~/Staphylococcus_aureus/shortjump_2.fastq \
-o Staphy1635c40
I strongly suggest that you try Ray v2.0.0-rc7, which has improvements
over v1.7.
Happy assembly !
Sébastien
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