Cuffmerge Error: Converting GTF files to SAM
0
0
Entering edit mode
6 weeks ago

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.

software error cufflinks cuffmerge • 115 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode

Thanks, my problem is solved.

ADD REPLY

Login before adding your answer.

Traffic: 1660 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6