HiSeq data processing with CASAVA1.7

[yongmei zhao]

Hi,

For those of you have HiSeq, would you please share some information about the computing requirement for data processing with CASAVA1.7? How long does it usually take for processing a 100 cycles PE run, 1 flowcell with GERALD pipeline in your computing environment? Number of cores(CPUs), RAM, disk space, tmp space allocated for running the job?

We experience much longer data processing time for HiSeq data than GAIIx data, and would like to know how other groups handle the increased volume of data from HiSeq. 

Thank you very much,

Yongmei

[Andrew Gagne]

Hi Yongmei,

Our validation run is still going.. would you provide your environment and run times?

andrew

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[Sivakumar Gowrisankar]

A 100PE takes between 1-2 days of processing. We use ELANDv2 by running them as separate jobs for each lane. Each gerald process is run on an 8 core node with 16GB mem (total), about 50 GB for /tmp.

Hope this helps.

[yongmei zhao]

Thank you for the responses.

In our case, A 100PE flowcell takes about 6 days of GERALD run time(using eland_pair) on a single node.  The process ran on an 8 core node with 16GB mem. 100GB of /tmp. If we have 8 nodes for running the jobs, the processing time will be very close to what Sivakumar provided here - about 1-2 days of processing time.

Thanks,

Yongmei