Running Ubuntu 14.04 on a 64 GB server, tried both CUDA 6.0 and 6.5 versions of balsa, all cuda sample executables run without error. Have been running soap3-dp on cuda 5.5.
Balsa is version from http://www.l3-bioinfo.com/balsa/web/index.php?r=site%2Fregister
Preparation went without error. Then
time ~/Downloads/balsax/balsa/balsa_cuda_6.0/balsa pair reference/mm10.fa.index mm10.snpDB mm10.indelDB mm10-gene-region-list.index fastq/index39_CTATAC_L001-L002_R1_001.fastq fastq/index39_CTATAC_L001-L002_R2_001.fastq result -b 3
Launching BALSA version 1.0. [BALSA] Analyzing read file for auto configuration. [BALSA] Detected max. read length : 106. [BALSA] Detected quality constant : +33.
...
I see this about 7 minutes into this alignment:
...
38 -> 38
39 -> 39
40 -> 40 [BALSA] Finish Score Recalibration Process [BALSA] Score Recalibration processing time ( including load reads ): 300.7750 seconds
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Running Ubuntu 14.04 on a 64 GB server, tried both CUDA 6.0 and 6.5 versions of balsa, all cuda sample executables run without error. Have been running soap3-dp on cuda 5.5.
Balsa is version from http://www.l3-bioinfo.com/balsa/web/index.php?r=site%2Fregister
Preparation went without error. Then
time ~/Downloads/balsax/balsa/balsa_cuda_6.0/balsa pair reference/mm10.fa.index mm10.snpDB mm10.indelDB mm10-gene-region-list.index fastq/index39_CTATAC_L001-L002_R1_001.fastq fastq/index39_CTATAC_L001-L002_R2_001.fastq result -b 3
Launching BALSA version 1.0.
[BALSA] Analyzing read file for auto configuration.
[BALSA] Detected max. read length : 106.
[BALSA] Detected quality constant : +33.
...
I see this about 7 minutes into this alignment:
...
38 -> 38
39 -> 39
40 -> 40
[BALSA] Finish Score Recalibration Process
[BALSA] Score Recalibration processing time ( including load reads ): 300.7750 seconds