error building nr database with prerapsearch

[pcantalupo]

Hello,

I'm on MacOSX 10.6 (snow leopard) and I successfully compiled rapsearch. But when I tried to build nr database I get following error.

$ ~/local/usr/local/rapSearch2/bin/prerapsearch -d nr.faa -n nr -s 14 &
now building hash file
terminate called after throwing an instance of 'boost::archive::archive_exception'
  what():  output stream error
[1]+  Abort trap              ~/local/usr/local/rapSearch2/bin/prerapsearch -d nr.faa -n nr -s 14

Is this a bug or did I do something wrong?

Thank you,

Paul

[zhaoyanswill]

Hi,

Did you compile boost serialization library by your self? Is that possible you disk is full? How long does this error occur after you type the command?

Sincerely, Y. Z.

On 04/02/2015 02:05 PM, pcantalupo wrote:

Hello,

I'm on MacOSX 10.6 (snow leopard) and I successfully compiled rapsearch. But when I tried to build nr database I get following error.

$ ~/local/usr/local/rapSearch2/bin/prerapsearch -d nr.faa -n nr -s 14 & now building hash file terminate called after throwing an instance of 'boost::archive::archive_exception' what(): output stream error [1]+ Abort trap ~/local/usr/local/rapSearch2/bin/prerapsearch -d nr.faa -n nr -s 14

Is this a bug or did I do something wrong?

Thank you,

Paul

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/16.

[pcantalupo]

Hello,

Sorry for late reply. My disk has 360GB. It is probably not the disk space Here are the exact command lines that I used to compile Rapsearch:

brew install boost
git clone https://github.com/zhaoyanswill/RAPSearch2
cd RAPSearch2/Src

# get rid of boost stuff in Rapsearch
rm -rf boost
rm -f libboost*

# copy our own boost stuff to Rapsearch
cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_chrono.a .
cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_serialization.a .
cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_system.a .
cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_thread-mt.a libboost_thread.a
cp -r /usr/local/homebrew/Cellar/boost/1.57.0/include/boost .

cd ..
install

Then, I tried to create the nr database. The command fails after about 5 minutes or so. It always seems to create an nr file that is 2,212,360,192 bytes in size.

Thank you for your help,

Paul

[zhaoyanswill]

Hi Paul,

Could you please try to test if the boost you installed works? I don't have MacOS machine, so I cannot tell what this error is. Thanks!

Sincerely, Y. Z.

On 04/06/2015 08:53 AM, pcantalupo wrote:

Hello,

Sorry for late reply. My disk has 360GB. It is probably not the disk space Here are the exact command lines that I used to compile Rapsearch:

|brew install boost git clone https://github.com/zhaoyanswill/RAPSearch2 cd RAPSearch2/Src

get rid of boost stuff in Rapsearch

rm -rf boost rm -f libboost*

copy our own boost stuff to Rapsearch

cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_chrono.a . cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_serialization.a . cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_system.a . cp /usr/local/homebrew/Cellar/boost/1.57.0/lib/libboost_thread-mt.a libboost_thread.a cp -r /usr/local/homebrew/Cellar/boost/1.57.0/include/boost .

cd .. install |

Then, I tried to create the nr database. The command fails after about 5 minutes or so. It always seems to create an |nr| file that is 2,212,360,192 bytes in size.

Thank you for your help,

Paul

— Reply to this email directly or view it on GitHub https://github.com/zhaoyanswill/RAPSearch2/issues/16#issuecomment-90051530.