RepeatScout make error

[yzzhang]

Hi, everyone. Now I get a assembled genome and I want to build a de novo repeat library using Repeatmodeler. However when I tried to install RepeatScoutV1.05, I typed make, but got warnnings,

zhang@localhost RepeatScout-1]$ make
cc -O3 -Wall -c build_repeat_families.c -o build_repeat_families.o
build_repeat_families.c: In function âmainâ:
build_repeat_families.c:137: warning: value computed is not used
build_repeat_families.c:161: warning: value computed is not used
cc -O3 -Wall -c cmd_line_opts.c -o cmd_line_opts.o
cc -O3 -Wall -c version.c -o version.o
cc build_repeat_families.o cmd_line_opts.o version.o -o RepeatScout -lm
cc -O3 -Wall -c build_lmer_table.c -o build_lmer_table.o
build_lmer_table.c: In function âmainâ:
build_lmer_table.c:85: warning: value computed is not used
cc build_lmer_table.o cmd_line_opts.o version.o -o build_lmer_table -lm


then this software did not work for me. Has some one face the same problem? How do you fix it? BTW, my computer system is redhat 5.
Many Thanks.
yun

[suryasaha]

Do you have the RepeatScout executable in the directory? If yes, try to run it using

./RepeatScout

[yzzhang]

Thank you for your quick reply. Yes, I can see the RepeatScout executable, but when I tried to run it with the sample data, I got the error:
[zhang@localhost RepeatScout-1]$ ./RepeatScout -sequence human3M.fa -freq human3M.freq -output test
Program duration is 64.0 sec = 1.1 min = 0.0 hr

so there may be some errors when the make command run. Still hope help me fix this problem. Thanks.
[
QUOTE=suryasaha;97840]Do you have the RepeatScout executable in the directory? If yes, try to run it using

./RepeatScout

[/QUOTE]

[suryasaha]

What is the exact error message? I presume you are following the instructions in the README file.

[yzzhang]

After I input the command ./RepeatScout -sequence human3M.fa -freq human3M.freq -output test

one minute later, there was a error showed,
Program duration is 64.0 sec = 1.1 min = 0.0 hr, no other information showed, could I find more information about the error from some file? I think the software was not complied correctly, right? Thank you.

[suryasaha]

Can you please list all the commands you have used (in order)? Thanks

[yzzhang]

actually, the first step build_lmer_table -l 14 -sequence human3M.fa -freq test.freq works.
then RepeatScout -sequence human3M.fasta -output test1 -freq test.freq -l 14 failed.

[suryasaha]

Try running this command and report the complete output

RepeatScout -sequence human3M.fa -output test1 -freq test.freq -l 14 -vvvv

The Fasta file name was incorrect. Is that what you used?

[yzzhang]

sorry, i typed the wrong name of human3M.fa. but added -vvvv it worked. Why added -vvvv it worked?
Actually, I used RepeatScout working for RepeatModeler to search for repeats denovo, I saw the RepeatMolder log, it said no models returned. "Program duration is 1071.0 sec = 17.9 min = 0.3 hr NOTE: RepeatScout did not return any models."
It is abnormal, do you know why? Many thanks.

[suryasaha]

The -vvvv is just verbose mode to make it print status messages. RepeatScout does find 165 repetitive sequences in the human3M set for me. They should be in the test1 file. I don't know how RepeatModeler interprets RepeatScout output, though.

[yzzhang]

Thank, suryasaha. I will try to use repeatscout directly for my assembly to see if the result is same as RepeatMoldeler log says. Many Thanks.

[priyanka_15]

Hi I am trying to run REpeatscout and when I reach to first filter stage it gives me error :
sh: 1: trf: not found
No such file or directory at ./filter-stage-1.prl line 110.

[suryasaha]

You don't have trf in your $PATH. Get it from here and put in your bin directory.

/home/your_username/bin

[priyanka_15]

Hello I did tried to put trf on my path but still it gives me the same error ..

CAn you suggest anything else ? I have attached a picture showing this

[suryasaha]

It looks like you did not export $PATH. Please make sure trf shows up on the command line before you run RepeatScout.