RepeatScout filtering errors

Question

[Chironex]

Hello everybody I was trying to use RepeatScout. I was following some steps one by one to analyze my sequences. Here there are the passages:

Repeatscout run: using fname.fa

1) ./build_lmer_table -l 15 -sequence fname.fa -freq fname.freq

2) ./RepeatScout -sequence fname.fa -output fnamescout.fa -freq fname.freq -l 14

Then the next step would be:

3) cat fnamescout.fa | ./filter-stage-1.prl> fnamescout_filtered.fa

but it reminds me this error:

sh: 1: trf: not found
No such file or directory at ./filter-stage-1.prl line 110.

I checked if TRF was installed, then I installed NSEG but it reminds again the same message. What's wrong?

[lieven.sterck]

and was TRF installed or not? Also make sure if is in your $PATH (== if correct you should be able to evoke it by simply typing trf on your commandline )

[Chironex]

Update: I've correctly installed TRF in /bin. So I tried to run the program but I generated a fasta file that is EMPTY. I think that I haven't correctly installed nseg. What is the correct location of nseg? I'm learning bioinformatic, so I have some trouble with nseg installation. Can I put it in /bin?

[lieven.sterck]

assuming that /bin will be in your $PATH, then yes you can install it there indeed

[Chironex]

I 've installed but the fasta output is still empty. I don't understand what's happening

[lieven.sterck]

and no message / runtime output while running the pipeline? If not then it's hard to resolve this