Question about running time of 30x WGS

[xiongl...@gmail.com]

Hi SMuFIn team:

It is great that there are mapping free structural variation calling program available. Your program is really easy to install. But I think I've run into some trouble and need your help.

I'm now running SMuFin on tumor&normal pair(each 30x) human WGS data. And it is difficult to upload the job to several nodes, so I use a large node, with 650g memory and 20 threads. I've run it for 24 hours, and nothing got.
By the way, node num needed according to your website seems to be: 2*3000*2.3*30/650000=0.65. Is it right?

The log file of running remains like this:
Checking input data files...
BWT index found for /Share/BP/xionglx/database/human/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa

The memory and cpu used is:
cpu=16:09:10, mem=10020.24963 GBs, io=0.00023, vmem=284.203M, maxvmem=284.203M

The command I used is:
SMuFin --ref /Share/BP/xionglx/database/human/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa --normal_fastq_1 30x_1_ultra_50ng.1.fq.txt --normal_fastq_2 30x_1_ultra_50ng.2.fq.txt --tumor_fastq_1 30x_1_390U.1.fq.txt --tumor_fastq_2 30x_1_390U.2.fq.txt --cpus_per_node 20 --patient_id 30x_1_390U.30x_1_ultra_50ng

Since I only use 1 node, so I do not use mpirun.

The question is:
Is there anything wrong as max memory used is only 284 Mb?
If yes, what should do to debug?
If not anything wrong, do you know how long it might take to get smufin output?

Looking forward to you reply.

Thank you.

Best,
Luoxing

[SMuFin]

Hi Luoxing,

First of all, can you check if you have full permissions on the human reference folder? SMuFin need them to do the execution.

The memory depends on the sample you use, but I think should be enough for a 30x sample, but if you have a chance to try it with a higher memory you should do it. Some cases, if the sample is complex, the memory increases.

SMuFin use openmpi to distribute the execution, so you should call SMuFin with it.

Regards,

[xiongl...@gmail.com]

Hi

Thanks for the reply.

The human reference folder is in my own path, and everything is fine when I use it in mapping. So there should be no problem with it.

I will rerun with openmpi and see if it is okay.

Thanks again.

Luoxing