Problems with cuffmerge

[Nnogueira]

0



Hi everyone,

I'm trying to use cuffmerge but I get the following error message:

[Thu Oct 27 13:47:16 2011] Converting GTF files to SAM [FAILED] Error: gtf_to_sam not found on this system. Did you forget to include it in your PATH?

My command line is:

/storage/app/cufflinks-1.0.3/cufflinks-1.0.3.Linux_x86_64/cuffmerge -g /storage/data/natasha/gtf/miRNA_related_tracks_known_miRNAs_hg18.gtf -s /storage/data/natasha/chrs_fa/hg18_no_random_no_hap.fa assembles_cancer.txt

I've tested the gtf_to_sam program and it works fine.

Do I have do put something else in my command line? I've read the manual, but I couldn't find anything...

thanks in advance!

[westerman]

How did you test the gtf_to_sam program? Please give the command line you used to do the test.

[ercfrtz]

I have fixed the issue.

[Nnogueira]

Hi,

thanks for the replys! I've already fixed it. It was a problem with my bash file, nothing to do with cufflinks... sorry!

To answer the other reply, my command line for testing the gtf_to_sam program was

cufflinks-1.0.3.Linux_x86_64/gtf_to_sam transcripts.gtf SRR04006_gtf2sam.sam

and it worked fine.

thanks again for the replys!

[westerman]

Glad you got it fixed. Just to help out people who may read this topic. I suspect that gtf_to_sam was not in your PATH. Thus the fix to your bash file as well as using a given path (cufflinks-1.0.3.Linux_x86_64) to start up the program.

[cewells]

clarification

I am having the same issue, i.e.

"Error:gtf_to_sam not found on this system. Did you forget to include it in your PATH?"

I have included the path to gtf_to_sam in my .bashrc file PATH variable, but still I get this error.

Any thoughts? I appreciate your help --

Christina

[jbrwn]

I am having the same issue, i.e.

"Error:gtf_to_sam not found on this system. Did you forget to include it in your PATH?"

I have included the path to gtf_to_sam in my .bashrc file PATH variable, but still I get this error.

Any thoughts? I appreciate your help --

Christina

what's the location of gtf_to_sam? what's your $PATH? did you source your bashrc or log out and back in?

[cewells]

With help from Cole Trapnell, I pinpointed the problem.

In case anyone runs into the same issue, gtf_to_sam should be specified in your PATH as:

PATH=$PATH:/home/cufflinks/ <or wherever you've stored gtf_to_sam>

Then I used

. ~/.bashrc

to reload the .bashrc file without logging out.

-Christina

[wangli]

Dear cewells

I defined the path in the command line.
But when I utilized .~/.bashrc, it showed that it cannot find the file or directory.
I used ls -a to see the hidden file, but no .bashrc.
Do you have an idea of this problem?
Thanks!

[westerman]

Dear cewells

I defined the path in the command line.
But when I utilized .~/.bashrc, it showed that it cannot find the file or directory.
I used ls -a to see the hidden file, but no .bashrc.
Do you have an idea of this problem?
Thanks!

Did you edit your .bashrc or just put the path on the command line?

The basic idea is to
1) Edit your .bashrc or .bash_profile to have the new PATH in it.

2) Either logout/login or source a 'source' or a '.' of the .bashrc or .bash_profile in order to read the file in and make the PATH change.


I should point out that doing the above is basic UNIX 101. You will not get far unless you understand how your shell gets set up in the first place.

[wanfahmi]

Hi,

I got an error when I am at the stage of merge using cuffmerge. Below is my error

$ cuffmerge -g genes.gtf -s genome.fa -p 4 assemblies.txt

[Mon Dec 3 15:23:23 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Mon Dec 3 15:23:23 2012] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/usr/local/cufflinks/cuffmerge", line 576, in <module>
sys.exit(main())
File "/usr/local/cufflinks/cuffmerge", line 538, in main
gtf_input_files = test_input_files(transfrag_list_file)
File "/usr/local/cufflinks/cuffmerge", line 268, in test_input_files
g = open(line,"r")
IOError: [Errno 2] No such file or directory: '1\tCufflinks\ttranscript\t89917\t91031\t1000\t-\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "0.6709083067"; frac "1.000000"; conf_lo "0.316487"; conf_hi "1.025329"; cov "2.502314";'


Please somebody help. Thank you!

[westerman]

Your 'assemblies.txt' file does not contain a list of files but rather contains data. At least that is my first guess.

[wanfahmi]

Hi Westerman,

Thanks for replying. do you mean the 'assemblies.txt' should have a list? Actually you are correct I guess as I did cat the all transcript.gtf. How should I do? Thanks

[westerman]

I do not do this too often and I am too busy at the moment to double-check but what you should have is a list of the individual files. E.g.,

cat >assemblies.txt
file1.gtf
file2.gtf
etc.

Not the contents of the files. The file names.

[wanfahmi]

Problems solved! thank you.

I did create a file that only contains the names not the contains of file. Its running.