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.
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.
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