cuffmerge stopped at Converting GTF files to SAM

[zhwang]

I was running cuffmerge and got the following message. it seem it stopped for some reason. Does anybody have ideas on what is going on?

[Thu Jul 19 11:38:15 2012] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Jul 19 11:38:15 2012] Preparing output location Documents/RNA_Seq/LSD1_analysis_072012/cuffmerge_07172012//
[Thu Jul 19 11:38:17 2012] Converting GTF files to SAM
buszczak-macpro:~ zwang$

[zhwang]

I have not fixed the problem, any suggestions would be much appreciated.

[rrichar]

cuffmerege

I am having the same problem. My error reads:

Mon Jul 23 09:35:33 2012] Converting GTF files to SAM
[09:35:33] Loading reference annotation.
Error: duplicate GFF ID 'ENST00000361547.2' encountered!
[FAILED]
Error: could not execute gtf_to_sam

I ran cuffcompare recently on the same gtf file and it worked, and simply warned of the GFF ID duplication, but did not fail.

Does anybody have an answer to this?

[zhwang]

I run the old version of cufflinks (last fall version) a couple of week ago and it was fine. After I have our computer guy updated the cufflinks to the most recent version, I start to encounter the problem even when running the same commands which had no problem at all before. My guess is that it should not be the files or commands problem but either the installation or compatibility issues.

[slockton]

I am having the same problem as zhwang. There is no error message on the command line nor in the log. I have no clue how to fix this!

[gechen]

Encountered the same problem. Found the access mode for gtf_to_sam is -rwx------. Changed that and it worked. Probably, the person who made the package messed it up.

[slockton]

THANK YOU gechen!

I can confirm that this solution worked. If anyone else has this problem locate gtf_to_sam, cd to its directory and use the command

chmod +xr gtf_to_sam

You might need to be root/use sudo to do this, depending on where gtf_to_sam has been installed.

Cheers,
S

[Sebastiann]

I am having the same problem as zhwang. There is no error message on the command line nor in the log. I have no clue how to fix this!

Persons with the same problem are reporting the same problem again and again but still till mow no one has got any responses friends if anyone of you get any answers then please PM me...

[cljkindgom]

I've encountered the sample problem, but when i used other's entry account to the server. the script worked well. Maybe there were some settings not right.