#29 SamToCA conversion failed

[Bright]

Hi, I had install PBcR with souce (wgs-8.3rc2.tar.bz2), but it failed at the step of "convertSamToCA". According to the log, it seemed the smrtanalysis is using old gcc library. I then changed to the dirctory and re-link the *so file. Although this worked for me, I wonder whether there are other methods?

Any suggestion would be grateful!

Fowllowing is what had I do:

1. Install gcc and exprot to PATH and LD_LIBRARY_PATH
   export PATH=/tools/gcc/destDir/bin:$PATH
   export LD_LIBRARY_PATH=/tools/gcc/destDir/lib64:/tools/gcc/gmp/destDir/lib:$LD_LIBRARY_PATH

2. Install PBcR
   bzip2 -dc wgs-8.3rc2.tar.bz2 | tar -xvf -
   cd wgs-8.3rc2/kmer
   make install >makeInstall.log 2>&1
   cd ../cd src
   make >make.log 2>&1

3. Install SMRT-Analysis
   SMRT_ROOT=/data7/lcy/zhongxm/tools/smrtanalysis
   SMRT_USER=lcy01
   SMRT_GROUP=mobile
   mkdir $SMRT_ROOT
   bash smrtanalysis_2.3.0.140936.run -p smrtanalysis-patch_2.3.0.140936.p4.run --rootdir $SMRT_ROOT

4. Running PBcR
   PBcR -threads 20 -length 500 -partitions 200 -l lambdaIll -s pacbio.SGE.spec -fastq pacbio.filtered_subreads.fastq genomeSize=50000 illumina.frg >log/pbcr.log 2>log/pbcr.err

5. The log
   SamToCA conversion failed
   /tools/wgs-8.3rc2/Linux-amd64/bin/convertSamToCA: /tools/smrtanalysis/current/analysis/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /tools/wgs-8.3rc2/Linux-amd64/bin/convertSamToCA)