I've installed Repeatscout from https://bix.ucsd.edu/repeatscout/. I've also installed TRF and nseg required by the program. I followed the steps:

build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq
 RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16

and the I put this command:

cat od_1000_repeats.fa| filter-stage-1.prl >od_1000_repeats_filt1.fa 

but this message appears:

bash: filter-stage-1.prl: command not found...

Why? It is all correctly installed, I can't understand the problem


1 Answer 1


If you're in the RepeatScout directory you need to execute the Perl script with a ./ prefix, like so.

cat od_1000_repeats.fa | ./filter-stage-1.prl > od_1000_repeats_filt1.fa

If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your $PATH environmental variable.

These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.

  • $\begingroup$ I installed repeatscout on my PC, I created the Repeatscout directory and It worked without errors. The problem is that it can't execute a file larger more than 800 mb in a 16 gb ram of my pc. So I had to use the cluster but I don't know where is the Repeatscout directory.(If I put "locate Repeatscout" I don't find it). I would to find the path to check if all the programs are correctly installed.. $\endgroup$
    – jonny
    May 1, 2019 at 17:18
  • $\begingroup$ It sounds like you need to get some help from your system administrator. $\endgroup$ May 1, 2019 at 18:12

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.