Hello Wei-Jen,
I don't think the error was caused by not providing the single-end reads.
From your logs, it says:
mpiexec: Warning: tasks 0-39,41-63 died with signal 15 (Terminated).
mpiexec: Warning: task 40 died with signal 11 (Segmentation fault).
What is the number of sequences in each file reported by Ray (see
NumberOfSequences.txt) ?
If you are using Open-MPI, you can use the command below to generate one
standard output file per MPI rank (there is 1 MPI rank per processor core).
mpiexec -n 64 \
-output-filename Test21 \
Ray -k 21 \
-o Test21 \
-p SRR131208_1.fastq SRR131208_2.fastq
You will get 64 standard output files named
Test21.1.00, Test21.1.01, ..., Test21.1.63.
With this, it will be easier to find the problem.
Also, you can compile Ray with
make ASSERT=y DEBUG=y PREFIX=DebugBuild
make install
To turn on runtime assertions.
Wei-Jen Chang a écrit :
> Hi Sebastien,
>
> Thanks so much for the comments
>
>
> Which version are you using ?
>
>
> I was using 2.0.0
>
>
> Is there something I did wrongfully?
>
>
> Can you provide the command you used to launch Ray ?
>
>
> I think this might be the problem. I used:
>
> mpiexec -np 64 Ray -k 21 -p /home/bio443/mtherkel/SRR131208_1.fastq
> /home/bio443/mtherkel/SRR131208_2.fastq -o Ray_test_06
>
> I apparently missed the -s part
>
>
> It should be something like:
>
> mpiexec -n 64 Ray -k 21 \
> -o Test21 \
> -s SRR131208.fastq \
> -p SRR131208_1.fastq SRR131208_2.fastq
>
>
> The assembly I got:
>
>
> Contigs >= 100 nt
> Number: 149053
> Total length: 75819372
> Average: 508
> N50: 822
> Median: 319
> Largest: 8701
> Contigs >= 500 nt
> Number: 54663
> Total length: 54570619
> Average: 998
> N50: 1068
> Median: 849
> Largest: 8701
> Scaffolds >= 100 nt
> Number: 140427
> Total length: 77365612
> Average: 550
> N50: 968
> Median: 290
> Largest: 16974
> Scaffolds >= 500 nt
> Number: 46037
> Total length: 56116859
> Average: 1218
> N50: 1466
> Median: 887
> Largest: 16974
>
>
>
> I will give it a try now!...:)
>
> Thanks,
>
> WJ
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