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Tandem Repeats Finder: a program to analyze DNA sequences

Home Page: https://tandem.bu.edu/trf/trf.html

License: GNU Affero General Public License v3.0

Makefile 14.96% C 67.95% Shell 16.80% M4 0.30%

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trf's Issues

Non-executable TRF

I am having a lot of pain trying to get TRF to work. No matter what I do or if I download the executable separate and move it in, I cannot get it to actually be executable. I even tried renaming it like was discussed in Dfam-consortium/RepeatModeler#20 as using TRF for RepeatMasker is my end goal. Would appreciate any help or guidance.

My code:

git clone https://github.com/Benson-Genomics-Lab/TRF.git
successfully downloads and shows up as TRF in my programs list
cd TRF
mkdir build
cd build
../configure
full output below
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking for ranlib... ranlib
checking whether ln -s works... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for library containing floor... -lm
checking for sqrt... yes
checking for memset... yes
checking for strchr... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
continuing on with the installation instructions
make
full output below
CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash /home/rbehm/Programs/TRF/missing aclocal-1.16
cd .. && /bin/bash /home/rbehm/Programs/TRF/missing automake-1.16 --gnu
CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash /home/rbehm/Programs/TRF/missing autoconf
/bin/bash ./config.status --recheck
running CONFIG_SHELL=/bin/bash /bin/bash ../configure --no-create --no-recursion
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking for ranlib... ranlib
checking whether ln -s works... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for library containing floor... -lm
checking for sqrt... yes
checking for memset... yes
checking for strchr... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
/bin/bash ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
(CDPATH="${ZSH_VERSION+.}:" && cd .. && /bin/bash /home/rbehm/Programs/TRF/missing autoheader)
rm -f stamp-h1
touch ../config.h.in
cd . && /bin/bash ./config.status config.h
config.status: creating config.h
config.status: config.h is unchanged
make all-recursive
make[1]: Entering directory '/home/rbehm/Programs/TRF/build'
Making all in src
make[2]: Entering directory '/home/rbehm/Programs/TRF/build/src'
gcc -DHAVE_CONFIG_H -I. -I../../src -I.. -fno-align-functions -fno-align-loops -g -O2 -MT trf-trf.o -MD -MP -MF .deps/trf-trf.Tpo -c -o trf-trf.o test -f 'trf.c' || echo '../../src/'trf.c
In file included from ../../src/trfrun.h:94,
from ../../src/trf.c:34:
../../src/trfclean.h: In function 'GetList':
../../src/trfclean.h:171:41: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
171 | for (counter =0; counter<9; counter++) fgets(hsequence, 255, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
../../src/trfclean.h:174:41: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
174 | for (counter =0; counter<3; counter++) fgets(hparameters, 255, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/trfclean.h: In function 'CleanAlignments':
../../src/trfclean.h:522:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
522 | fgets(string2, 260, al_fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/trfclean.h:523:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
523 | fgets(string3, 260, al_fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/trfclean.h:541:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
541 | fgets(string2, 260, al_fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/trfclean.h: In function 'BreakAlignments':
../../src/trfclean.h:606:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
606 | fgets( headlns[i], 200, al_fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../src/trfclean.h:632:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
632 | fgets(buffer, 200, al_fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h: In function 'TRF':
../../src/trfrun.h:727:25: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
727 | sprintf(htmlstring,"%s.%s.html",paramset.outputprefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 525 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:728:25: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
728 | sprintf(txtstring ,"%s.%s.txt.html",paramset.outputprefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 11 and 529 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:729:25: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
729 | sprintf(datstring ,"%s.%s.dat",paramset.outputprefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 524 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:730:25: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
730 | sprintf(maskstring,"%s.%s.mask",paramset.outputprefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 525 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h: In function 'TRFControlRoutine':
../../src/trfrun.h:342:20: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
342 | sprintf(desth,"%s.%s.summary.html",prefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 15 and 533 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:355:21: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
355 | sprintf(destm,"%s.%s.mask",prefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 525 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:369:22: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
369 | sprintf(destd,"%s.%s.dat",prefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 524 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:420:20: warning: '.s' directive writing 2 bytes into a region of size between 1 and 260 [-Wformat-overflow=]
420 | sprintf(input,"%s.s%d",prefix,i);
| ^~
../../src/trfrun.h:420:17: note: directive argument in the range [1, 2147483647]
420 | sprintf(input,"%s.s%d",prefix,i);
| ^~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 272 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:512:21: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
512 | sprintf(outh,"%s.%s.1.html",input,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 9 and 527 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:535:26: warning: '.s' directive writing 2 bytes into a region of size between 1 and 260 [-Wformat-overflow=]
535 | sprintf(maskstring,"%s.s%d.%s.mask",prefix,i,paramstring);
| ^~
../../src/trfrun.h:535:23: note: directive argument in the range [1, 2147483647]
535 | sprintf(maskstring,"%s.s%d.%s.mask",prefix,i,paramstring);
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 537 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:544:20: warning: '.s' directive writing 2 bytes into a region of size between 1 and 260 [-Wformat-overflow=]
544 | sprintf(outm,"%s.s%d.%s.mask",prefix,i,paramstring);
| ^~
../../src/trfrun.h:544:17: note: directive argument in the range [1, 2147483647]
544 | sprintf(outm,"%s.s%d.%s.mask",prefix,i,paramstring);
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 537 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:308:27: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
308 | sprintf(maskstring,"%s.%s.mask",paramset.outputprefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 525 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:220:44: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
220 | sprintf(destd,"%s.%s.dat",prefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 524 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../src/trf.c:34:
../../src/trfrun.h:308:27: warning: '%s' directive writing up to 259 bytes into a region of size between 0 and 259 [-Wformat-overflow=]
308 | sprintf(maskstring,"%s.%s.mask",paramset.outputprefix,paramstring);
| ^~ ~~~~~~~~~~~
In file included from /usr/include/stdio.h:867,
from ../../src/trf.c:28:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 525 bytes into a destination of size 260
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mv -f .deps/trf-trf.Tpo .deps/trf-trf.Po
gcc -fno-align-functions -fno-align-loops -g -O2 -o trf trf-trf.o -lm
make[2]: Leaving directory '/home/rbehm/Programs/TRF/build/src'
make[2]: Entering directory '/home/rbehm/Programs/TRF/build'
make[2]: Leaving directory '/home/rbehm/Programs/TRF/build'
make[1]: Leaving directory '/home/rbehm/Programs/TRF/build'
now I want to test the installation to see if it all worked using the samples provided
trf test_seqs.fasta 2 5 7 80 10 50 2000 -l 10
but I get an error!
Command 'trf' not found, did you mean:
command 'tlf' from deb tlf (1.4.0-2)
command 'tjf' from deb pvm-examples (3.4.6-2build2)
command 'trs' from deb konwert (1.8-13build1)
command 'tr' from deb coreutils (8.30-3ubuntu2)
command 'tf' from deb tf (1:4.0s1-20build1)
command 'tf' from deb tf5 (5.0beta8-7)
command 'erf' from deb xoreos-tools (0.0.5-1build4)
command 'trn' from deb trn4 (4.0-test77-12)
Try: apt install

It doesn't matter which directory I run this line in TRF, TRF/build, TRF/build/src I get the same error.
Please help!

Add length of sequence input to .dat file?

Hi,

Do you think future versions might include the input sequence length in the .dat file? This would facilitate post-processing of .dat file for repeat content estimation within a sequence

The input sequence length seems to be reported in the .html files but not in the .dat file

Many thanks for TRF!

Thomas

output length of tandem repeats

Hi, I am trying to figure out how to estimate the total length of tandem repeats found in a sequence and I can't figure out which metric to use. I have several genomes I would like to analyse, I would be interested in how to generate this data from TRF output, do you have any recommendation ?

trf2bed

Is there a recommended or vetted output convert to make a bed file from the trf output?
e.g. trf2bed.py

I've found one online, not sure if works. Are there better ways?

Would you please "Inverted Repeats Finder" or open its source?

Hi, Prof. Hernandez
I'm install a package which depends on "Inverted Repeats Finder", however I can't download Inverted Repeats Finder 3.07 for Linux.
There is a message "Error Message. A system error occurred. Please go back and try the download again. Could not read data from file
irf307.linux.download.count: If this error persists send an email message to [email protected]". And Inverted Repeats Finder 3.05 for Linux didn't work on my system (ubuntu 18). So I wrote to you for some help.
Best regards!

TRF on protein sequence

Hi there!

I am studying the proteome of a non model species and I would like to annotate repetitive sequences in proteins. I was wondering if TRF coud work on the protein sequence instead of nucleotide sequence.

Best regards,
Giulia

sequence size

I have a sequence length is more than 2 gigabase?it turns out buffer over flow?

Running in multiple fasta files

Hi there. I have folders with many fasta files and when I use this:

# usr/bin/env bash

for fasta in Genomes_new/"$1"/"$2"/"$3"/CHR/*_chr.fna; 
do
 #echo "$fasta"
  trf "$fasta" 2 7 7 80 10 50 500 -h; 
done

But I got only one file and then trf finishes. Do you have any suggestion to get all fasta files done?
Paulo

Links to 4.09.1 files seem to contain 4.10.0-rc.2

The current links to files labeled as from the 4.09.1 release seem to actually be 4.10.0-rc.2 files. For example, the configure script has the 4.10.0-rc.2 string in a number of places. Presumably there are incorrect links on github.

longer tandem repeat identification

I'm interested in identifying tandem repeats longer than 2kb. Have been reading through the original paper and the code to understand the current upper bound; iiuc the main limitation is based on the extent of the simulation data that's included in the init_and_fill_coin_toss_stats2000_with_4tuplesizes() function. If I run my own simulations to generate longer waitdata and sumdata arrays, could that allow detection of repeats with periods of say 10kb or am I missing other challenges?

last four column of the output

There are four columns with sequences in the output tabular file. It seems no document about these sequences.

@seq8
35738 35771 16 2.1 16 88 0 50 11 23 0 64 1.26 TTCTTCATCTTTTAAC TTCTTCTTCTTTTTACTTCTTCATCTTTTAACTT AGTAACTGAACGATTATGATTTTACTGTAATATATCTACTACAAGTTTTT TCTCTTTAAATCTCATATGAAGATGATAAAACACATCAATGGAGGAAAGA

I wonder what these sequences are?
Thank you.

Time consuming process

Hi There,
I am trying to use TRF to detect tandem repeats in a large genome assembly with the size of 2.68 Gb. Although the program worked for about 12 days on a node with 32 CPUs and 125 Gb memory, finally it was not completed. The following is the command I have used:
trf new_id.fasta 2 5 7 80 10 50 2000
Is there any way to improve the efficiency of the computation? e.g parallel processing or reduce the computation time . I would be appreciated if you could help me in this regard.
Thank you

exit code 146

I was trying to run this cmd inside my (slurm) script

trf genome.fasta 2 7 7 80 10 50 500 -d -m -h

It was running fine producing output files until it got to the end. It aborted silently without saying what caused the error.

I already asked the sysadmins and they say that do not report any kill signal by the scheduler on that job AND that it must have been the tool itself that generated that exit code and then quit execution.

I am attaching the log file of the execution progress
slurm-7224411.out.txt

A little bit of background:

This genome is giving us trouble. It is an insect. The BUSCOS for the genome are above 95%; however, the BUSCOS for the (BRAKER2) proteins is under 5%. We cannot figure out what is causing this discrepancy. That why we are exploring the possibility of tandem repeats confounding the genome annotation tool.

Context dependence of calls for short repeats

I am having issues with TRF (version 4.09) missing multiple short homopolymers.

I've produced an example below with a (modified) sequence from the yeast genome that contains two motifs with period size 1 and a copy number of 6. Both motifs are detected in the first sequence, but single-nucleotide changes outside the repeat result in trf not reporting either the first or the second sequence, depending on the change.

The command I am calling is
trf test.fa 2 7 7 80 10 8 1000 -h -d -ngs

The contents of test.fa (with the inserted nucleotides capitalized) are:

>seq_find_both
gacgtagcaatccaaaaaagggaagtctaggcgccccccaccg
>seq_miss_first
Tgacgtagcaatccaaaaaagggaagtctaggcgccccccaccg
>seq_miss_second
gacgtagcaatccaaaaaagggaagtctaggcgTccccccaccg

Is this behavior expected? Is there any way to modify it?

Thank you!

- Eugene

TRF v4.10.0 on miniconda

Dear all,
I'm currently integrating TRF in a NextFlow pipeline. Although I've been previously able to use TRF v4.0.9 successfully outside of such framework, it seems I am now facing an issue due to non zero exit status in absence of any errors. In fact, NextFlow is using the exit code to evaluate whether the pipeline execution should stop or not, and it stops when the exit status is not 0. I found in the README:
"TRF now has an exit status of 0 on success, and non-zero otherwise. Previously, TRF would have a non-zero exit status which was to be interpreted by the user as the number of TRs processed.".
Based on this sentence, I think having a conda v4.10.0 installation for TRF should solve the issue. I already tried compiling from source, but with no success. Could you please update the conda version?
Thanks,
Simone

Issue about tandem repeat GAA in FXN gene missed by TRF.

Hi, I am new to this fantastic tool TRF.
When I explore GAA tandem repeats in FXN gene (responsible for a neurogenetic disease, Friedreich ataxia) using UCSC "simple repeats" track, I found this motif "GAA" is not recognized by TRF. I am confused about this.

Could anyone help me with this issue? Thank you!

The locus (hg38):
chr9:69037261-69037304

Installation issue

Hi, I'm having some trouble installing TRF to use with RepeatModeller, and I'm hoping you might be able to give some advice on how to fix this. I'm running macOS High Sierra v10.13.6 on my MacBook Pro.

In the terminal I cloned the repository using:

git clone https://github.com/Benson-Genomics-Lab/TRF.git

Then I moved to the directory, made a build subdirectory and within that, compiled:

cd trf-4.10.0 mkdir build cd build ../configure

This didn't throw up any warnings or errors, the output was:

checking build system type... x86_64-apple-darwin17.7.0
checking host system type... x86_64-apple-darwin17.7.0
checking target system type... x86_64-apple-darwin17.7.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ../install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking for ranlib... ranlib
checking whether ln -s works... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for library containing floor... none required
checking for sqrt... yes
checking for memset... yes
checking for strchr... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands

After this I ran:

make

And then a number of warnings and errors return:

/Library/Developer/CommandLineTools/usr/bin/make all-recursive
Making all in src
gcc -DHAVE_CONFIG_H -I. -I../../src -I.. -fno-align-functions -fno-align-loops -g -O2 -MT trf-trf.o -MD -MP -MF .deps/trf-trf.Tpo -c -o trf-trf.o test -f 'trf.c' || echo '../../src/'trf.c
clang: warning: optimization flag '-fno-align-functions' is not supported [-Wignored-optimization-argument]
clang: warning: optimization flag '-fno-align-loops' is not supported [-Wignored-optimization-argument]
In file included from ../../src/trf.c:34:
In file included from ../../src/trfrun.h:92:
../../src/tr30dat.h:365:25: error: use of undeclared identifier '_MAX_PATH'
char inputfilename[_MAX_PATH]; /* constant defined in stdlib /
^
../../src/tr30dat.h:366:24: error: use of undeclared identifier '_MAX_PATH'
char outputprefix[_MAX_PATH];
^
../../src/tr30dat.h:367:27: error: use of undeclared identifier '_MAX_PATH'
char outputdirectory[_MAX_PATH];
^
../../src/tr30dat.h:368:26: error: use of undeclared identifier '_MAX_PATH'
char outputfilename[_MAX_PATH];
^
In file included from ../../src/trf.c:34:
../../src/trfrun.h:309:57: warning: passing 'unsigned char ' to parameter of type 'char ' converts between pointers to integer types with different sign
[-Wpointer-sign]
MakeMaskedFile(GlobalIndexList, paramset.maskedfile, Sequence, maskstring);
^~~~~~~~
../../src/trfclean.h:878:54: note: passing argument to parameter 'Sequence' here
void MakeMaskedFile(IL
headptr,int masked,char
Sequence,char
maskfile)
^
In file included from ../../src/trf.c:34:
../../src/trfrun.h:536:57: warning: passing 'unsigned char ' to parameter of type 'char ' converts between pointers to integer types with different sign
[-Wpointer-sign]
MakeMaskedFile(GlobalIndexList, paramset.maskedfile, Sequence, maskstring);
^~~~~~~~
../../src/trfclean.h:878:54: note: passing argument to parameter 'Sequence' here
void MakeMaskedFile(IL
headptr,int masked,char
Sequence,char* maskfile)
^
In file included from ../../src/trf.c:34:
../../src/trfrun.h:795:11: warning: assigning to 'unsigned char *' from 'char ' converts between pointers to integer types with different sign
[-Wpointer-sign]
Sequence = pseq->sequence-1; /
start one character before */
^ ~~~~~~~~~~~~~~~~
../../src/trfrun.h:926:42: warning: passing 'unsigned char ' to parameter of type 'char ' converts between pointers to integer types with different sign
[-Wpointer-sign]
paramset.datafile,paramset.maskedfile,Sequence,maskstring);
^~~~~~~~
../../src/trfclean.h:100:44: note: passing argument to parameter 'Sequence' here
int maxsize, int data, int masked, char
Sequence,
^
../../src/trf.c:120:28: error: initializer element is not a compile-time constant
{"dat", no_argument, &paramset.datafile, 1}, /
-d, -D */
^~~~~~~~~~~~~~~~~~
../../src/trf.c:322:21: error: use of undeclared identifier 'dirsymbol'
while(i>0&&*pname!=dirsymbol)
^
../../src/trf.c:327:13: error: use of undeclared identifier 'dirsymbol'
if(*pname==dirsymbol) pname++;
^
4 warnings and 7 errors generated.
make[2]: *** [trf-trf.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

I don't think it has properly installed, because when looking in the src sub-directories in /build and the TRF master directory, I can't find a file called trf (only trf.c):

'$ pwd'
~/TRF/build
'$ ls'
Makefile config.h config.log config.status src stamp-h1
'$ ls src/'
Makefile
'$ ls ..'
AUTHORS Makefile.in build configure install-sh
COPYING NEWS compile configure.ac missing
ChangeLog README config.guess depcomp src
INSTALL README.md config.h.in history.txt t
Makefile.am aclocal.m4 config.sub images_for_readme test_seqs.txt
'$ ls ../src/'
Makefile.am Makefile.in tr30dat.c tr30dat.h trf.c trfclean.h trfrun.h

If anybody could help me troubleshoot, I would be very grateful! I'm not very savvy when it comes to compiling and installing within terminals, so sorry if I've overlooked something simple!

Thanks,

Rob

Test suite failures for other architectures than amd64

Hi,
thanks to your very welcome step to free the source code of trf the Debian Med team has included the package into main Debian. Nilesh Patra has written a test suite for it to verify its functionality in a continuous integration test. Here you can see the actual test that is run. This works all well on amd64 architecture. However, Debian builds all packages also for 12 other official architectures (and more inofficial). Not all of those architectures are just running the test suite. On the package overview page you see marked with red that arm64, armhf and i386 are not passing the test. When having a look into the i386 test log (please scroll down to the end or seek for the keyword I'm quoting) there is an error (its the same as in amd64 - but there the explicit hint for the error is missing. No idea why):

Scanning Sequence 3...
Freeing Memory...
Resolving output...
Done.
Loading sequence file...
Allocating Memory...
Error: Unable to allocate 1745033308 bytes for stemp array. Please set a lower value for the longest TR length. (trfrun.h:649)

I was able to reproduce the very same error message on arm64. Thus I inspected the code and it seems that I've found the parameter to tweak to work around this explicit error in a patch. By decreasing the MAXBANDWIDTH parameter to 32 (I've checked 64 but than it fails) the error simply changes to:

Scanning Sequence 3...
.

.

testbed failure: testbed auxverb failed with exit code 255

Before I might start some debugging I wonder whether reducing the MAXBANDWIDTH parameter that far might make any sense or whether the more simple approach to declare TRF for amd64 only and not build it for any other architecture at all would be the more simple approach.
Kind regards, Andreas.

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