Problem in mapping on SHRiMP 2

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

• 1,860 views • link

updated 3.6 years ago by Ram

• written 11.1 years ago by Muhammad Ilyas •

1 answer

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

• 0 views • link

updated 3.6 years ago by Ram

• written 11.1 years ago by Pierre Lindenbaum