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Old 02-28-2013, 10:32 AM   #1
yzzhang
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Default RepeatScout make error

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 āmainā:
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 āmainā:
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
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Old 02-28-2013, 10:50 AM   #2
suryasaha
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Do you have the RepeatScout executable in the directory? If yes, try to run it using
Code:
./RepeatScout
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Old 02-28-2013, 11:07 AM   #3
yzzhang
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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
Code:
./RepeatScout
[/QUOTE]
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Old 02-28-2013, 11:28 AM   #4
suryasaha
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What is the exact error message? I presume you are following the instructions in the README file.
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Old 02-28-2013, 11:40 AM   #5
yzzhang
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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.
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Old 02-28-2013, 11:44 AM   #6
suryasaha
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Can you please list all the commands you have used (in order)? Thanks
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Old 02-28-2013, 11:54 AM   #7
yzzhang
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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.
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Old 02-28-2013, 12:00 PM   #8
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Try running this command and report the complete output
Code:
RepeatScout -sequence human3M.fa -output test1 -freq test.freq -l 14 -vvvv
The Fasta file name was incorrect. Is that what you used?
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Old 02-28-2013, 12:12 PM   #9
yzzhang
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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.
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Old 02-28-2013, 12:16 PM   #10
suryasaha
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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.
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Old 02-28-2013, 12:21 PM   #11
yzzhang
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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.
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Old 10-01-2015, 01:19 PM   #12
priyanka_15
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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.
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Old 10-01-2015, 02:30 PM   #13
suryasaha
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You don't have trf in your $PATH. Get it from here and put in your bin directory.

/home/your_username/bin
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Old 10-01-2015, 02:53 PM   #14
priyanka_15
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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
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Old 10-01-2015, 05:24 PM   #15
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It looks like you did not export $PATH. Please make sure trf shows up on the command line before you run RepeatScout.
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Old 10-02-2015, 11:17 AM   #16
priyanka_15
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Default Tried to export PATH but still not worrking

Hi

I tried exporting the PATH But it is still not working ..PIctures attched
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File Type: png Screenshot from 2015-10-02 12:11:22.png (107.9 KB, 2 views)
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Old 10-02-2015, 11:23 AM   #17
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If trf is the file the program is trying to execute then $PATH directory declaration needs to end at the level of the directory which contains the trf file (e.g. /path_to/repeatscout/RepeatScout-1). Open a new terminal, re-export PATH and try again.

Last edited by GenoMax; 10-02-2015 at 11:28 AM.
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Old 10-02-2015, 11:32 AM   #18
priyanka_15
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ok , one more question should this be permanent ? because every time I close terminal it goes back to previous PATH..

I am new to this all ,perl,linux and repeatscout ; may be these are very easy questions
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Old 10-02-2015, 11:38 AM   #19
priyanka_15
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Hello

I tried to do what you said ,is this the way ? It still is not reading the trf file
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Old 10-02-2015, 11:47 AM   #20
GenoMax
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Two questions.

1. Have you compiled the software by doing "make" in this directory?
2. I see the following help when I try to run RepeatScout. Are you trying to follow directions given by someone/some website?

EDIT: I see that you are on step three of this process. You are trying to process the output of RepeatScount like this?

Quote:
$ cat repeats.fa | filter-stage-1.prl > repeats-filtered.prl

Last edited by GenoMax; 10-02-2015 at 11:57 AM.
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