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Old 06-17-2011, 06:24 AM   #1
Junior Member
Location: Evry, France

Join Date: Jun 2011
Posts: 1
Default Casava 1.7 slowness


We notided that the Casava 1.7 software take 3 days to demultiplex a paired-end run (2x51) where only 3 lanes was indexed. He spent two days on not indexed lanes (so, normally, just to rename the read3 to read2 I think ?) (config : Linux/Red Hat Sun Fire X4140 server with 2 CPU AMD Opteron 2384 quadri-core, RAM 64 GB ... parallelization 'make -8' used).

Apparently, there is a problem with the "demultiplexTile" program , which apparently spent 50% of its CPU time to do the system command "stat" :

stat("./001/s_7_1_0041_qval.txt.gz.tmp", 0x7fff85fea4e0) = -1 ENOENT (No such file or directory)
stat("/env/export/nfs9/solexa/TRANSFERT/110406_MERCURE_B01LEABXX/Data/Intensities/BaseCalls/s_7_1_0041_qval.txt.gz", 0x7fff85fea6e0) = -1 ENOENT (No such file or directory)
stat("/env/export/nfs9/solexa/TRANSFERT/110406_MERCURE_B01LEABXX/Data/Intensities/BaseCalls/s_7_2_0041_qval.txt.gz",0x7fff85fea6e0) = -1 ENOENT (No such file or directory)

Illumina's tech support solved my problem with an incremental version of this software include in the CASAVA-1.7.1a5 package.

This version is actually much more efficient : 2 hours instead of 3 days

I don't know if I am an isolated case ... maybe this will help some of you

FredG is offline   Reply With Quote
Old 06-17-2011, 07:28 AM   #2
Location: Montreal

Join Date: Oct 2009
Posts: 63

I solved that problem in january after 2 weeks of thinking our nfs server was collapsing. One email to tech support fixed it.

I would have liked for them to acknowledge the problem and notify their clients about it. Oh well, Casava 1.8 is out now, so back to the drawing board.
lletourn is offline   Reply With Quote

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