SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RepeatScout make error yzzhang Bioinformatics 33 08-23-2016 12:22 AM
RepeatModeler genomic assembly BuildDatabase error antoza Introductions 2 04-11-2016 06:50 PM
RepeatModeler Error (eleredef failed. Exit code 768) fahmida Bioinformatics 2 08-12-2015 04:50 PM
RepeatModeler FastaDB::getSubstr error klduong Bioinformatics 3 07-20-2014 09:35 AM
RepeatModeler Error fahmida Bioinformatics 3 07-23-2013 12:21 AM

Reply
 
Thread Tools
Old 08-19-2016, 04:02 AM   #1
zhanghao
Member
 
Location: BEIJING

Join Date: Nov 2015
Posts: 17
Smile RepeatScout and RepeatModeler error

I want to use RepeatScout working for RepeatModeler to search for repeats. When I installed RepeatScout, I used "make" command according to README. But it is showed many warning beleow:
bac@bac-X10DAi:~/RepeatScout-1$ make
cc -O3 -Wall -c build_repeat_families.c -o build_repeat_families.o
build_repeat_families.c: In function ‘main’:
build_repeat_families.c:137:36: warning: value computed is not used [-Wunused-value]
co_get_int(argc, argv, "-l", &l) || (l = default_l(MAXLENGTH));
^
build_repeat_families.c:161:62: warning: value computed is not used [-Wunused-value]
co_get_float(argc, argv, "-maxentropy", &MAXENTROPY) || (MAXENTROPY=-0.7);
^
build_repeat_families.c:174:19: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
master[2*L+l] = (char)NULL;
^
build_repeat_families.c: In function ‘mask_headptr’:
build_repeat_families.c:1026:28: warning: variable ‘flip’ set but not used [-Wunused-but-set-variable]
int x, y, smallh, h, h2, flip;
^
build_repeat_families.c: In function ‘build_headptr’:
build_repeat_families.c:389:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp,"%s",string);
^
build_repeat_families.c:390:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp,"%d",&thisfreq);
^
build_repeat_families.c:391:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
fscanf(fp,"%d",&thisocc);
^
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 ‘main’:
build_lmer_table.c:85:36: warning: value computed is not used [-Wunused-value]
co_get_int(argc, argv, "-l", &l) || (l = default_l(MAXLENGTH));
^
build_lmer_table.c:51:10: warning: variable ‘start’ set but not used [-Wunused-but-set-variable]
time_t start;
^
cc build_lmer_table.o cmd_line_opts.o version.o -o build_lmer_table -lm

I try to test it with example:
./build_lmer_table -l 14 -sequence human3M.fa -freq test.freq
./RepeatScout -sequence human3M.fa -output test1 -freq test.freq -l 14
It showed "Program duration is 22.0 sec = 0.4 min = 0.0 hr" no other information. And I can find the output file test1 with 165 sequences.

However, in RepeatModeler, it failed "NOTE: RepeatScout did not return any models". and in round 1, the file sampleDB-1.fa.rscons.filtered is empty.

I do not know what wrong with it.
zhanghao is offline   Reply With Quote
Old 08-23-2016, 12:04 AM   #2
Macspider
Member
 
Location: Vienna

Join Date: Feb 2016
Posts: 35
Default

Hey,
First, when you make and it throws out warnings like unused-value, it doesn't mean that it automatically doesn't work (it can be). Sometimes these are warnings because some of the dependencies of the program are newer or older than the ones around which it was built, and thus maybe certain variables become deprecated but it still tries to declare them. At the end of the compiling script there is a block to check which variables are declared but not used, so here is why the warning. It is good to pay attention to this, though, because sometimes it might brake something. For what concerns RepeatScout, I guess the problem is more in your input files than in the compiling process.

May I ask you what are you providing, and to paste here the command you ran?
Macspider is offline   Reply With Quote
Old 02-02-2017, 11:29 PM   #3
jhju
Junior Member
 
Location: korea

Join Date: Feb 2017
Posts: 1
Default

I have same errors!
Even though there are not any errors, the consensi.fa file is empty
Did you solve them?

Last edited by jhju; 02-03-2017 at 10:18 PM.
jhju is offline   Reply With Quote
Reply

Tags
repeatmodeler, repeatscout

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:30 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO