Question: Problem in mapping on SHRiMP 2
gravatar for Muhammad Ilyas
4.5 years ago by
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

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 • 1.0k views
ADD COMMENTlink modified 4.5 years ago by Pierre Lindenbaum124k • written 4.5 years ago by Muhammad Ilyas0
gravatar for Pierre Lindenbaum
4.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

the variable  $SHRIMP_2_2_3 is not defined


is then resolved to



set the variable or use a relative path


or fix the ${PATH} :



ADD COMMENTlink written 4.5 years ago by Pierre Lindenbaum124k
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