Cuffmerge Error: Converting GTF files to SAM

Question

[sahar.salimi92]

Hi, I run cuffmerge -g hg38_refseq.gtf -s chrX.fa -p 8 assemblies.txt command but I get the following error

[Wed Feb 24 22:07:24 2021] Beginning transcriptome assembly merge
-------------------------------------------

[Wed Feb 24 22:07:24 2021] Preparing output location ./merged_asm/ [Wed Feb 24 22:07:25 2021] Converting GTF files to SAM   [FAILED] Error: gtf_to_sam not found on this system.  Did you forget to include it in your PATH?

What should I do to solve this problem?

Thanks for your help.

[swbarnes2]

Well...is cufflinks in your path? Did you google the problem? Did you already try everything here? http://seqanswers.com/forums/showthread.php?t=15092

[sahar.salimi92]

Yes, I did.

(base) sahar@sahar-VirtualBox:~/project/chr22$ export PATH=$PATH:/apps/cufflinks-2.2.1.Linux_x86_64
(base) sahar@sahar-VirtualBox:~/project/chr22$ source ~/.bashrc
(base) sahar@sahar-VirtualBox:~/project/chr22$ echo $PATH
/home/sahar/anaconda3/bin:/home/sahar/anaconda3/condabin:/home/sahar/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/lib/jvm/java-15-oracle/bin:/usr/lib/jvm/java-15-oracle/db/bin:/apps/cufflinks-2.2.1.Linux_x86_64

[Mensur Dlakic]

If you have done all that, typing which gtf_to_sam should give the following output:

/apps/cufflinks-2.2.1.Linux_x86_64/gtf_to_sam

If not, verify that the file is in that location:

ls -al /apps/cufflinks-2.2.1.Linux_x86_64/gtf_to_sam

[sahar.salimi92]

Thanks, my problem is solved.