cuff merge does not run

Question

[AGA]

Hi all,

I am trying to run Cuffmerge after 2-3 years and for whatever reason I cannot run it anymore. I am using the correct command line:

cuffmerge -g genes.gtf -s genome.fa -p 12 assemblies.txt

and it starts running:

[Fri Apr 14 16:15:50 2017] Beginning transcriptome assembly merge
-------------------------------------------

[Fri Apr 14 16:15:50 2017] Preparing output location ./merged_asm/
[Fri Apr 14 16:16:02 2017] Converting GTF files to SAM
[16:16:02] Loading reference annotation.
[16:16:08] Loading reference annotation.
[16:16:15] Loading reference annotation.
[16:16:21] Loading reference annotation.
[Fri Apr 14 16:16:28 2017] Quantitating transcripts

Once it gets to "Quantitating transcripts" step, stays there forever and I can see nothing is running. I tried with cufflinks-2.1.1 and cufflinks-2.2.1 versions, and I get exactly the same problem. Can someone help to me with this problem?

Thanks,

[GenoMax]

stays there forever and I can see nothing is running

How long in terms of actual time and how are you determining that nothing part?

[AGA]

I had one running for 6-7 hours and I could see in the the process was "sleeping". this happens in the moment "Quantitating transcripts" step starts. Until that point everything looks fine and no error shows up no before no after that. In the tmp folder in the output I can see that the last file created was mergeSam_tmp.4.Saw7no. I even tested just with 2 samples and the same happened, when it should not take that long, but i get the same result.

PID    COMMAND      %CPU  TIME     #TH    #WQ  #PORT MEM    PURG   CMPRS  PGRP  PPID  STATE    BOOSTS             %CPU_ME %CPU_OTHRS UID  FAULTS
50074  cufflinks    0.0   00:00.00 1      0    13    612K   0B     0B     50067 50067 sleeping *0[1]              0.00000 0.00000    501  1335
50067  python2.7    0.0   00:12.52 1      0    13    5864K  0B     0B     50067 49978 sleeping *0[1]              0.00000 0.00000    501  4501

Thanks,

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

[Petr Ponomarenko]

By any chance could you please share with us the files or at least parts of files that reproduce the problem? Is there any chance your reference is not the one used for the gtf?

[WouterDeCoster]

You should know that Tophat/cufflinks/cuffmerge/duffdiff is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. (If you can't get access to that publication, let me know and I'll -cough- help you.)

[AGA]

Thanks, I know they are in low maintenance, but since cuff merge is running locally i thought i would not have any problem with it. I will check the paper you recommended. Thanks a lot.