CUffDIFF fatal exit code Error 139

Question: CUffDIFF fatal exit code Error 139

3.4 years ago by

michimaurin • 20 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 • 2.7k views

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modified 3.4 years ago • written 3.4 years ago by michimaurin • 20

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link modified 3.4 years ago • written 3.4 years ago by michimaurin • 20

3.4 years ago by

michimaurin • 20

michimaurin • 20 wrote:

Done let me know if you all got it :)

ADD COMMENT • link written 3.4 years ago by michimaurin • 20

3.4 years ago by

michimaurin • 20

michimaurin • 20 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 COMMENT • link written 3.4 years ago by michimaurin • 20

In review, will reply shortly. Jen

ADD REPLY • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

3.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

3.4 years ago by

michimaurin • 20

michimaurin • 20 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

ADD COMMENT • link written 3.4 years ago by michimaurin • 20

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 REPLY • link modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link modified 3.4 years ago • written 3.4 years ago by michimaurin • 20

3.4 years ago by

michimaurin • 20

michimaurin • 20 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 COMMENT • link written 3.4 years ago by michimaurin • 20

3.4 years ago by

michimaurin • 20

michimaurin • 20 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 COMMENT • link written 3.4 years ago by michimaurin • 20

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