Question: Problem in mapping on SHRiMP 2
0
gravatar for Muhammad Ilyas
3.8 years ago by
Pakistan
Muhammad Ilyas0 wrote:

I have install shrimp 2 in my Linux system by command line that is given in read me file, 
following command are 

 $ tar xvzf SHRiMP_2_2_3.lx26.x86_64.tar.gz
  $ cd SHRiMP_2_2_3
  $ file bin/gmapper
  bin/gmapper: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for
  GNU/Linux 2.6.9, statically linked, for GNU/Linux 2.6.9, not stripped
  $ export SHRIMP_FOLDER=$PWD

than I start mapping genome with reference using following command 
 $SHRIMP_2_2_3/bin/gmapper-cs DRR0000_2.fasta \
  ciona.fa \
  -N 4 -o 5 -h 80% >map.test1.out 2>map.test2.log

I got empty .out file and map.test2.log file getting following error
bash: /bin/gmapper-cs: No such file or directory


As I am a beginner and recently used this software kindly provide me some guidance which can help me solve this problem.

sequencing genome • 891 views
ADD COMMENTlink modified 3.8 years ago by Pierre Lindenbaum118k • written 3.8 years ago by Muhammad Ilyas0
1
gravatar for Pierre Lindenbaum
3.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

the variable  $SHRIMP_2_2_3 is not defined

 $SHRIMP_2_2_3/bin/gmappep

is then resolved to

/bin/gmappep

 

set the variable http://www.cyberciti.biz/faq/linux-unix-shell-export-command/ or use a relative path http://www.linuxnix.com/2012/07/abslute-path-vs-relative-path-in-linuxunix.html

 

or fix the ${PATH} : http://www.linfo.org/path_env_var.html

 

 

ADD COMMENTlink written 3.8 years ago by Pierre Lindenbaum118k
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