On CASAVA
09 Jun 2012官网注册帐号后就可以下载，最新的1.8.2已经支持每个样品输出一组FastQ文件。
编译安装运行都不需要root权限，以前在BIOPIC听她们说跑CASAVA必须root权限我还奇怪了些许……
贴个命令行备案：
/opt/CASAVA/bin/configureBclToFastq.pl --input-dir /bak/seqdata/original/120523_SN483_0244_BC0M01ACXX/Data/Intensities/BaseCalls --output-dir /bak/seqdata/raw/120523_SN483_0244_BC0M01ACXX --sample-sheet /bak/seqdata/original/0244_BC0M01ACXX-SS.csv --no-eamss --with-failed-reads --fastq-cluster-count -1 --mismatches 1 --tiles s_[78] 2>do.err
cd /bak/seqdata/raw/120523_SN483_0244_BC0M01ACXX
make -j23 -l23.5 >make.txt 2>make.err &
--fastq-cluster-count -1就是设置只输出一组.fq.gz的。其实/Data/Intensities/BaseCalls/下的.bcl文件已经是只有最好碱基(2bit)与质量值(6bit)的东西了，所以，安装通常的RTA直接在Windows下出碱基来看的话，CASAVA就是转格式与按index拆分而已。那个--mismatches 1就是设置index上的mismatch数，默认是0。
不过./Data/Intensities/L00[1-8]/s_*.clocs是CASAVA需要的，只是旁边的*.cif和*_T.FWHMMap可以不要。
make时其实只会每个fq出一个进程，就是说，PE的FlowCell最多16进程同时跑。
由于.bcl文件是每Cycle一个，所以内存够大的话，缓存能把运行时间缩小5倍多（大致估的）。
然后，运行时看到：
[configureBclToFastq.pl] WARNING: 'LocationFileType' element not found in .../Data/Intensities/BaseCalls/../RTAConfiguration.xml
网上找到 解答：
I actually asked tech support about this, here is their answer:
Hi Louis,
This warning message you see is due to a slight incompatibility between RTA/OLB versions and CASAVA 1.8 standard requirements and there should not be any issues during data analysis as it is not an error message.
Regards,
Sid
-----<Email Received>-----
From: ..
Sent: 6/26/2011 12:18 PM PDT
To: techsupport@illumina.com
CC:
Subject: configureBclToFastq.pl warning
When running configureBclToFastq.pl I got this:
WARNING: 'LocationFileType' element not found in
/data/hiseq67/110617_SN909_0050_BD040RACXX_0047HS11B/Data/Intensities/BaseCalls/../RTAConfiguration.xml
What can we do to remove this warning?
It's not an important warning but I just want to make sure we fill out
everything in case.
Thanks
Louis
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