cufflinks get stuck in proceed

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6.6 years ago

sxm891114 • 0

hi,

have you met the problem:

cufflinks get stuck when processing locus

I tried several times but got stuck in the same position.

I had 2 sample and 3 repeats each, 6 files in all. the former 4 runned smoothly, problem happened from the 5th file.

I have no idea what happened.

do you think redo build--tophat2 and re-paste .gff file can help?

thanks

RNA-Seq cufflinks • 1.3k views

ADD COMMENT • link 6.6 years ago by sxm891114 • 0

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Are you sure that it is stuck? Sometimes, Cufflinks appears to be doing nothing when, in fact, it is working hard. You can open another terminal and use the top command to see if the process is still running.

ADD REPLY • link 6.6 years ago by Kevin Blighe 88k

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yes, it was still occupying CPU and memory. I don't know why those 2 files runned so slowly that seem stuck during proceeding. I should have done it at server, maybe my computer memories is not enough for. So I decided to use hisat2-stringtie-ballgown instead of it, whose speed was extremely higher than that. thank you~

ADD REPLY • link 6.6 years ago by sxm891114 • 0

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