TGICL using

[zhuyan]

Hello everyone:

when I use the tgicl, I encounter a problem :
"Process terminated with an error, at step 'Initialization'! "

my command line is : ./tgicl -F ~/tmp/test.fa

The error in file err_tgicl_test.fa.log as follows:
>>> --- Initialization [/home/zhuy/tmp/test.fa] started at Apr 24 13:52:54 2012
tgicl.nozmsort.pl running options:
tgicl.nozmsort.pl /home/zhuy/tmp/test.fa
Standard log file: tgicl_test.fa.log
Error log file: err_tgicl_test.fa.log
Using 1 CPUs for clustering and assembly
Path is : /home/zhuy/bin/RNA/denovo_2.0/tgicl/bin:/home/zhuy/bin/RNA/denovo_2.0/tgicl:/home/zhuy/local/perl/bin:/home/zhouzh/lib/jdk1.6.0_23/bin:/home/zhuy/
-= Rebuilding /home/zhuy/tmp/test.fa indices =-
Error at cdbfasta /home/zhuy/tmp/test.fa

Process terminated with an error, at step 'Initialization'!
tgicl.nozmsort.pl (/home/zhuy/tmp/test.fa) encountered an error at step Initialization
Working directory was /home/zhuy/bin/RNA/denovo_2.0/tgicl.

Thank you !

[sklages]

Is your fasta file correct? Maybe you can post the first few entries.It seems that indexing your sequences failed (cdbfasta).

[zhuyan]

Thank you, sklages!

I think my fasta file is all right, and it can be normally formatdb.

Also, I change another fasta file coming from NCBI Genome database, but the error still exist.

[arvid]

What error message do you get when you execute

cdbfasta /home/zhuy/tmp/test.fa

It might be that cdbfasta doesn't like your fasta file, even though BLAST formatdb can handle it. Try to modify the identifiers in your fasta file (first I'd make sure that the first space-delimited part is unique, since this is the default identifier used by cdbfasta) and run the cdbfasta utility manually, outside of tgicl, until it accepts your fasta file.

[zhuyan]

Thank you for your advice, arvid!

When I type '/home/zhuy/bin/cdbfasta test.fa',

bash: /home/zhuy/bin/cdbfasta: No such file or directory. This is maybe the reason,

but the file 'cdbfasta' is existing, and the file permission is: -wxr-xr-x, the path'/home/zhuy/bin/' is also included in my $PATH.

I don't known why has this problem?

[arvid]

Please type the following commands:

ls -al /home/zhuy/bin/cdbfasta
ls -al /home/zhuy/bin/RNA/denovo_2.0/tgicl/bin/cdbfasta

and report the output. The error you've posted says that cdbfasta doesn't exist there... I'd guess that you find the cdbfasta executable in /home/zhuy/bin/RNA/denovo_2.0/tgicl/bin, according to the TGICL log in your first post. If it's in $PATH (as well indicated in the log), just typing "cdbfasta" should be enough. ~/bin/ is typically in $PATH, but you can check this with

echo $PATH

[sklages]

What linux are you using?

If the binary is really present, try

ldd /home/zhuy/bin/cdbfasta

and see if the linux loader is found ...

I had such kind of problems with custom made linux and some pre-compiled binaries (years ago though).

[zhuyan]

What linux are you using?

If the binary is really present, try

and see if the linux loader is found ...

I had such kind of problems with custom made linux and some pre-compiled binaries (years ago though).

My linux is : "Linux version 2.6.32-21-generic, Ubuntu 10.04"

When I type "ldd /home/zhuy/bin/cdbfasta"
-------- not a dynamic executable

but type "file /home/zhuy/bin/cdbfasta", it shows:
"ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.2.5, stripped"

I don't know what this mean?

Thank you !

[sklages]

My linux is : "Linux version 2.6.32-21-generic, Ubuntu 10.04"

When I type "ldd /home/zhuy/bin/cdbfasta"
-------- not a dynamic executable

but type "file /home/zhuy/bin/cdbfasta", it shows:
"ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.2.5, stripped"

I don't know what this mean?

Thank you !

That's strange.

I get:

bin $ file cdbfasta 
cdbfasta: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), 
dynamically linked (uses shared libs), for GNU/Linux 2.2.5, stripped

bin $ ldd cdbfasta
    linux-gate.so.1 =>  (0xffffe000)
    libm.so.6 => /project/mariux32/i686/tools/lib/libm.so.6 (0xf773b000)
    libc.so.6 => /project/mariux32/i686/tools/lib/libc.so.6 (0xf75dc000)
    /lib/ld-linux.so.2 (0xf7761000)

What is the output of arvids proposed commands (ls)?

[zhuyan]

Code:

$ ls -al /home/zhuy/bin/cdbfasta
-rwxr-xr-x 1 zhuy zhuy 113180 2012-04-24 11:21 /home/zhuy/bin/cdbfasta

$ ls -al /home/zhuy/software/TGICL-2.1/bin/cdbfasta
-rwxr-xr-x 1 zhuy zhuy 113180 2010-11-13 02:23 /home/zhuy/software/TGICL-2.1/bin/cdbfasta

It looks normal !

[arvid]

Code:


It looks normal !

Indeed it does... I have no idea why it won't run on your machine... Maybe the executable got corrupted somehow. You could try to unpack the installation archive again and reinstall it. Otherwise I'd try to contact the authors (might be tricky since it is quite old).

[sklages]

Hmm, now we have just another 'cdbfasta'? (Which apparently has been built/installed on 2010-11-13). So what happens when you type :

which cdbfasta
ldd /home/zhuy/software/TGICL-2.1/bin/cdbfasta
/home/zhuy/software/TGICL-2.1/bin/cdbfasta test.fa

[zhuyan]

I unpack the installation archive again and re-install it.

$ /home/zhuy/bin/cdbfasta
bash: /home/zhuy/bin/cdbfasta: Accessing a corrupted shared library

$ ldd /home/zhuy/bin/cdbfasta
not a dynamic executable

It looks as if there are something wrong with my library files.

[arvid]

Try to re-install the shared libraries cdbfasta is relying on (see post #9) with the Ubuntu package manager (in case you have corrupted something with a manual installation)... or you might want to try to run it on a machine with an older Linux distro, or a RedHat-type one (like Fedora or CentOS). I've been able to successfully run TGICL on Fedora 14-16 and CentOS 5.x (didn't try on 6.x, yet).

[sklages]

I unpack the installation archive again and re-install it.
It looks as if there are something wrong with my library files.

What is "/home/zhuy/software/TGICL-2.1/bin/cdbfasta"?

When I download the current TGICL, extract the files and run:

$ ldd ./cdbfasta
    linux-gate.so.1 =>  (0xffffe000)
    libm.so.6 => /project/mariux32/i686/tools/lib/libm.so.6 (0xf76e4000)
    libc.so.6 => /project/mariux32/i686/tools/lib/libc.so.6 (0xf7585000)
    /lib/ld-linux.so.2 (0xf770a000)

I do get an output. I can even run that tool without error.

This is a pretty up-to-date linux system. What ditribution are you using?