error message of cuffmerge

[dzmtnvmt]

Hi,

When running cuffmerge, I only got very implicit error messages. It seemed that the gtf files were converted into sam files, but then stuck.

I tried to troubleshot in several aspects: checking the name of chromosome(with chr or not); sorting the gtf files (chr name then coordinate); with larger memories. But none of them helped. I'm wondering if any of you might also meet this.

Any suggestion will be helpful, thanks.


=============command and message====================
$ cuffmerge -g dmel-all-r6.09.gtf -s dmel_chr_r609.fa assemblies.txt

[Sun Feb 21 17:29:11 2016] Beginning transcriptome assembly merge
-------------------------------------------

[Sun Feb 21 17:29:11 2016] Preparing output location ./merged_asm/
[Sun Feb 21 17:29:14 2016] Converting GTF files to SAM
[17:29:14] Loading reference annotation.
[17:29:16] Loading reference annotation.
[17:29:17] Loading reference annotation.
[17:29:18] Loading reference annotation.
[Sun Feb 21 17:29:19 2016] Quantitating transcripts
You are using Cufflinks v2.2.1, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g
../../../dmelGenomes/dmel-all-r6.09.gtf -q --overhang-tolerance 200
--library-type=transfrags -A 0.0 --min-frags-per-transfr
ag 0 --no-5-extend -p 1
./merged_asm/tmp/mergeSam_fileTqiEXC
[17:29:19] Loading reference annotation.
[17:29:23] Inspecting reads and determining fragment length distribution.
[FAILED]
Error: could not execute cufflinks

[GenoMax]

I assume you have run cufflinks already so the program must be installed and working on your machine. Simplest explanation may be that you do not have "cufflinks" program in your $PATH/current directory. You can amend your $PATH variable and then re-run.

[dzmtnvmt]

Thanks, GenoMax. But this is not the reason, I'm sure cufflinks is in the PATH. I also tried "cufflinks -o ./merged_asm/ -F 0.05 -g
../../../dmelGenomes/dmel-all-r6.09.gtf -q --overhang-tolerance 200
--library-type=transfrags -A 0.0 --min-frags-per-transfr
ag 0 --no-5-extend -p 1" separately, the message is more concise:

=========
[11:45:13] Loading reference annotation.
[11:45:17] Inspecting reads and determining fragment length distribution.
Segmentation fault

[GenoMax]

It looks like cufflinks is seg faulting/crashing. Which could be because of many reasons. Have you used this copy of cufflinks before?

[dzmtnvmt]

The version of cufflinks is v2.2.1. I loaded it as a module in a computing cluster (and all commands of the cufflinks package were loaded), so I think the software is correctly located and functional.

I mainly used cuffdiff to estimate differently expressed annotated genes before, and didn't use cuffmerge often.

[GenoMax]

Not sure what to tell you in this case. Since someone else installed this program we should assume that they built the program from source or got the right binary for this OS.

You are sure there is no other cufflinks in $PATH from an older version that may be getting preferentially executed.

[dzmtnvmt]

I think this is the only version available. Thank you, GenoMax, all the same.

[dzmtnvmt]

Hi GenoMax, I finally found the problem is caused by the cufflinks (v2.2.1) in the cluster. And when using an earlier version (v2.2.0) by myself, it all went well.

Thanks, and sorry for bothering.