cufflinks "waiting for 1 threads to complete"

[letusgo]

Hi,
I used tophat as my mapping tool and I got a .bam file. Then ,I used cufflinks to got the transcript.gtf file.But when I run cufflinks , it told me that:

[19:16:03] Assembling transcripts and initializing abundances for multi-read correction.
> Waiting for 1 threads to complete. [************************ ] 99%

then I wait a long time. But it still stay here. How can I do next?

Thank you

[sdriscoll]

that's happened to me before. i've waited it out and it does eventually complete. the only other thing you can do is cancel it and start over.

[letusgo]

that's happened to me before. i've waited it out and it does eventually complete. the only other thing you can do is cancel it and start over.

i had done this several times, but it still didn't work completely. when you start it again,does it complete?

[sunqiwei]

i had done this several times, but it still didn't work completely. when you start it again,does it complete?

I also have this problem “Waiting for 1 threads to complete. [************************ ] 99%” ，and wait a long time.
Have you run this successfully, how you run it?

Hope your reply, thank you!

[letusgo]

I also have this problem “Waiting for 1 threads to complete. [************************ ] 99%” ，and wait a long time.
Have you run this successfully, how you run it?

Hope your reply, thank you!

yeah, but I even don't know why, I just restarted it and waited. Maybe you can set -m and -s manually, then try it again.
good luck~

[jb2]

Also running into this issue with a lot of my jobs getting stuck at 99% (using Cufflinks 2.0.2). Has anyone figured out this issue?

[jb2]

I'm finding that over time all my jobs finish, but for some reason some get stuck here for much longer than other jobs, some running for five days with no movement before the thread finishes. I'm still wondering why that is.