Cuffdiff error usr/lib64.libz.so.1

[jamminbeh]

Hello, When I ran Cuffdiff, I get the following error:

cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff)

All the files come out ok, except the cds files are empty. Do you know how to fix this error, and are the other results files ok? Thanks a lot.

[shurjo]

Hello, When I ran Cuffdiff, I get the following error:

cuffdiff: /usr/lib64/libz.so.1: no version information available (required by cuffdiff)

All the files come out ok, except the cds files are empty. Do you know how to fix this error, and are the other results files ok? Thanks a lot.

http://seqanswers.com/forums/showthread.php?t=8042&highlight=libz.so.1

[jamminbeh]

Hello, So you don't think that this file has anything to do with getting empty cds files? Thank you.

[jdjax]

Hello,

I am receive the same error message as discussed in this thread. But I do not understand your answers and have no idea how to fix it. Can either one of you please explain in further detail what is the problem and now to fix it.

I am running cufflinks v1.0.3 on a hp server with RHEL 5.4. and I am not sure if cufflinks was built or the binary was downloaded since the post doc in the group installed this program. I would appreciate your help in this matter. Thanks in advance.


[jadf@flseq sorted]$ cufflinks -o trial trinity_n_trial_inflorescence.sorted.bam
cufflinks: /usr/lib64/libz.so.1: no version information available (required by cufflinks)
You are using Cufflinks v1.0.3, which is the most recent release.
Warning: BAM header too large
File trinity_n_trial_inflorescence.sorted.bam doesn't appear to be a valid BAM file, trying SAM...

[jadf@flseq lib64]$ ls -l | grep libz
-rwxr-xr-x 1 root root 108692 Jul 19 2006 libz.a
lrwxrwxrwx 1 root root 13 Jul 25 2010 libz.so -> libz.so.1.2.3
lrwxrwxrwx 1 root root 13 Jul 25 2010 libz.so.1 -> libz.so.1.2.3
-rwxr-xr-x 1 root root 85928 Jul 19 2006 libz.so.1.2.3

[vyellapa]

I'm getting a similar error and even if I ignore the "libz.so.1" error as I have a newer version, I cannot make sense as to why it cannot create the directory. I have the file permissions to create directory. Any ideas?

cuffdiff: /lib64/libz.so.1: no version information available
(required by cuffdiff)
Warning: Could not connect to update server to verify current version.
Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Error: cannot create directory /scratch/vyellapantula/RNA/cuffVedge/ARDARP

[g781]

Hello,

I have the same warning message (error?). I surveyed previous information, but no one said it's okay for sure.

Does anyone have the same message but run your samples as well?

[vyellapa]

basically cufflinks accepts relative file paths. So instead of /scratch/vyellapa/cufflinks give ./cufflinks from /scratch/vyellapa.

[g781]

Hi vyellapa

Thanks your answer. Unfortunately, the warning message is the same.
Anyway, I am going to test cufflinks on two operating systems, CentOS 6 and CentOS 5.6, without and with warning, respectively.

If the results are the same, I can run the data without any concern. Although I am not really sure whether or not the test is correct, I still can get some information to people.

I will share it later.

Thanks

[g781]

Hi all,

I am just done with a test in comparison cufflinks (one of functions in Cufflinks pipeline) binary with source code and summarize as below.

All tests used the same sample.

Binary code:
1. It was tested in 3 PCs with CentOS5.6 and CentOS6.0.
2. Results are the same.

Source code (complied by myself):
1. It was tested only in 1 PC with CentOS6.0 due to problems of compiling Cufflinks pipeline in other PC with CentOS5.6.
2. I ran cufflinks on sample twice.
3. Results are the same.

Binary vs Source code:
1. Both results are almost the same. If I have to say a number, it's probably around 97-99%.

If you would like to check it, please download the results as a following link:

https://dl.dropbox.com/u/32178068/comparision.rar