G Rendon - 2013-11-14

I compiled pBWA on a cray system that uses cray-mpich2 rather than mpich2-gnu.
It seemed to run fine on the first test run. I used 4 nodes. Each node has 32 cores. I just used half of them for the test (t 16).
The problem is that I see four different files created for aln reads1 reads2 and for sampe.
Why? What do I do with the four sam files now: combine them?

Thanks in advance for your help.

The command line for pBWA aln looks like this for reads1

aprun -n 4 -d 32 /projects/sciteam/jou/builds/pBWA_1.21009/pBWA aln -t 16 -f /projects/sciteam/jou/Benchma
rk_PBWA_n4_d32_t16/0926000593.FCD0D3CABXX_L1_.R1.sai /projects/sciteam/jou/mayo_novo/allchr.fa /projects/s
citeam/jou/BioBank/0926000593.FCD0D3CABXX_L1_R1.fastq

The command line for pBWA sampe lloks like this

aprun -n 4 -d 1 /projects/sciteam/jou/builds/pBWA_1.21009/pBWA sampe -f /projects/sciteam/jou/Benchmark_PB
WA_n4_d32_t16/0926000593.FCD0D3CABXX_L1_.4.32.sam /projects/sciteam/jou/mayo_novo/allchr.fa /projects/scit
eam/jou/Benchmark_PBWA_n4_d32_t16/0926000593.FCD0D3CABXX_L1_.R1.sai /projects/sciteam/jou/Benchmark_PBWA_n
4_d32_t16/0926000593.FCD0D3CABXX_L1_.R2.sai /projects/sciteam/jou/BioBank/0926000593.FCD0D3CABXX_L1_R1.fas
tq /projects/sciteam/jou/BioBank/0926000593.FCD0D3CABXX_L1_R2.fastq

This is a partial list of the content of the output folder

ls -la Benchmark_PBWA_n4_d32_t16
total 91792868
drwxrws--- 2 rendong ILL_jou 4096 Nov 14 13:07 .
drwxrws--- 15 victorj ILL_jou 4096 Nov 14 11:20 ..
-rw------- 1 rendong ILL_jou 22062790373 Nov 14 13:07 0926000593.FCD0D3CABXX_L1_.4.32.sam-00000.sam
-rw------- 1 rendong ILL_jou 22079161742 Nov 14 13:07 0926000593.FCD0D3CABXX_L1_.4.32.sam-00001.sam
-rw------- 1 rendong ILL_jou 22085052406 Nov 14 13:07 0926000593.FCD0D3CABXX_L1_.4.32.sam-00002.sam
-rw------- 1 rendong ILL_jou 22087524257 Nov 14 13:07 0926000593.FCD0D3CABXX_L1_.4.32.sam-00003.sam
-rw------- 1 rendong ILL_jou 716600824 Nov 14 11:56 0926000593.FCD0D3CABXX_L1_.R1.sai-1-00000.sai
-rw------- 1 rendong ILL_jou 719208200 Nov 14 11:56 0926000593.FCD0D3CABXX_L1_.R1.sai-1-00001.sai
-rw------- 1 rendong ILL_jou 719111088 Nov 14 11:56 0926000593.FCD0D3CABXX_L1_.R1.sai-1-00002.sai
-rw------- 1 rendong ILL_jou 720082976 Nov 14 11:52 0926000593.FCD0D3CABXX_L1_.R1.sai-1-00003.sai
-rw------- 1 rendong ILL_jou 698009032 Nov 14 11:57 0926000593.FCD0D3CABXX_L1_.R2.sai-1-00000.sai
-rw------- 1 rendong ILL_jou 700517352 Nov 14 11:57 0926000593.FCD0D3CABXX_L1_.R2.sai-1-00001.sai
-rw------- 1 rendong ILL_jou 702237504 Nov 14 11:57 0926000593.FCD0D3CABXX_L1_.R2.sai-1-00002.sai
-rw------- 1 rendong ILL_jou 703814336 Nov 14 11:54 0926000593.FCD0D3CABXX_L1_.R2.sai-1-00003.sai