Question: CUffDIFF fatal exit code Error 139
1
gravatar for michimaurin
2.5 years ago by
michimaurin20
michimaurin20 wrote:

Hi My cuffdiff run does not continue , it stops and says  FATAL error exit code 139(), 
My function parameters are 
Condition I 2 replicate bam files ( my replicate alignments) 
Condition II 2 replicate bam files ( my second set of replicate alignments or second experimental conditioN)
GTF file provided was actually produced by cuffmerge of the GTF files generated from cufflinks is 0.3 Gigs
Each bam file is between 6-7 Gigs 
I would appreciate any kind of help
Michelle 

rna-seq software error galaxy • 1.9k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by michimaurin20
1
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Where are you working? If http://usegalaxy.org, please send in a bug report that includes a link to this post and we can review/provide feedback. If not working on Main, please see if you can replicate this there or send in more about the reported error message.

Just so you know, conditions should be named with alphanumeric characters and (optionally) underscores, no spaces. Also, segmentation faults can indicate that a tool requires more compute resource than is available to the process (the job running the tool).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson23k

I am using usegalaxy.org server tried using both the default server and the regular server and both came back with the same error , I submitted the bug report along with this link , thanks a lot I deeply appreciate your help 

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by michimaurin20
0
gravatar for michimaurin
2.5 years ago by
michimaurin20
michimaurin20 wrote:

Done let me know if you all got it :)

ADD COMMENTlink written 2.5 years ago by michimaurin20
0
gravatar for michimaurin
2.5 years ago by
michimaurin20
michimaurin20 wrote:

One more comment , the spaces added here for the identifiers were not included in the actual run , the actual run has no spaces 

ADD COMMENTlink written 2.5 years ago by michimaurin20

In review, will reply shortly. Jen

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson23k
0
gravatar for Jennifer Hillman Jackson
2.5 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The tool is a confirmed mismatch for the tool form. A github issue has been opened to correct the tool form. Progress on the correction can be followed here: https://github.com/galaxyproject/tools-devteam/issues/170

Thank you for reporting the issue and sending in an example. For now, the jobs you have running with a single BAM input is the proper usage (meaning, ignore the option to submit multiple). But if you have any problems with that, please let us know.

We appreciate the detective work! Jen, Galaxy team

ADD COMMENTlink written 2.5 years ago by Jennifer Hillman Jackson23k
0
gravatar for michimaurin
2.5 years ago by
michimaurin20
michimaurin20 wrote:

Jen !

So Technically  I cannot use the galaxy , for differential expression if I have replicates , is that what I read??

I just want to make sure so I can give feedback to "my boss"

Thanks 

 

MM

ADD COMMENTlink written 2.5 years ago by michimaurin20

No, you can definitely use replicates with this pipleline. Just do the Cufflinks and Cuffquant steps on the individual samples. Cuffmerge then combines them all into the reference GTF. Finally, put all together in conditions as replicates on the Cuffdiff tool form along with the Cuffmerge GTF result. This is basically the same RNA-seq pipeline as was used earlier, with an extra normalization step (via Cuffquant).

Does this help? Jen

 

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson23k
Jen! tried cuff Quant already , and got the run of one of the samples to give me output but it does not give me a gtf file so , how do I do cuffmerge on it and use it at cuff diff, is there a place I can read on this?I have been watching David coil youtube videos , but on this point they do not help me much.;) Thanks again
ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by michimaurin20
0
gravatar for michimaurin
2.5 years ago by
michimaurin20
michimaurin20 wrote:

Cool will do the reading on cuffcuant  to see what kind of parameters to give and will give it a shot. Thanks for sticking around ;)

ADD COMMENTlink written 2.5 years ago by michimaurin20
0
gravatar for michimaurin
2.5 years ago by
michimaurin20
michimaurin20 wrote:

I know this might be very technical, but I rather ask, what is the difference between the gtf file that comes from cuff merging the files out of cufflinks, vs, the gtf file that would be got out of cuffcuant?my guess is that it's an aditional step in the normalization or something . Thanks a lot all this has been an eye opener for me 

ADD COMMENTlink written 2.5 years ago by michimaurin20
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