Help: cufflinks stopped in one loci

[lewewoo]

I used cufflinks to estimate gene expression in a gtf file, however, one sample could not pass one loci, always stopped there (all the other samples are fine); the command i used is as following:
cufflinks -G XXX.gtf YYY.bam
the error information is as following:
You are using Cufflinks v1.1.0, which is the most recent release.
[18:37:04] Loading reference annotation.
[18:37:04] Inspecting reads and determining fragment length distribution.
> Processing Locus chr21:9825743-9826389 [************* ] 52%

this lasts for ever and I then changed --max-bundle-frags to 2000000, but still stoppped here; after that I went to gtf file to find the loci and deleted this loci, now it stopped in another loci, what should I do? delete another loci? helps please!!!

[lewewoo]

Then I tried:
cufflinks YYY.bam
(I plan to try cuffcompare YYY.gtf XXX.gtf later)

it stopped in another loci...anything wrong with my .bam??? please help...

[lewewoo]

all stopped, because bam is too big so cufflinks crashed? please help, thanks!

[joyce kang]

Have you solved the problem? I have the same problem with you. Please help us!!!!!

[lewewoo]

my solution is waiting....if the terminal window is still working, do nothing just wait.... other samples only 2hours, this sample needs overnight...dont know why .... good luck!

[joyce kang]

I also tried cufflinks and it also stops. When I leave it and waited it, there will be "processing stop" appeared on the terminal. Do you see this problem?


Thanks!

[lewewoo]

no, i did not see that, can you post all the command and response message here? maybe can know what happened...

[smowton]

Hi,

Obviously this thread is quite old, but if experiencing a similar problem you might want to try the patch (and patched binaries) described here: https://groups.google.com/forum/#!to...rs/UzLCJhj3lUE

Please let me know if this resolves the situation!

Chris